diff --git "a/src/extract_data.ipynb" "b/src/extract_data.ipynb" new file mode 100644--- /dev/null +++ "b/src/extract_data.ipynb" @@ -0,0 +1,4575 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### 1. Download the dataset from https://ptmint.sjtu.edu.cn/data/PTM%20experimental%20evidence.csv into CSV_PATH = \"../data/ptmint_dataset.csv\"" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### 2. Scrape complex names and features from website" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import requests\n", + "from bs4 import BeautifulSoup\n", + "import time\n", + "import os" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Done: AANAT\n", + "Done: AATF\n", + "Done: ABCG2\n", + "Done: ABI1\n", + "Done: ABI3\n", + "Done: ABL1\n", + "Done: ABRAXAS1\n", + "Done: ABRAXAS2\n", + "Done: ACACA\n", + "Done: ACAP1\n", + "Done: ACE\n", + "Done: ACE2\n", + "Done: ACKR3\n", + "Done: ACOT4\n", + "Done: ACTB\n", + "Done: ACTN1\n", + "Done: ACTN4\n", + "Done: ADAM22\n", + "Done: ADD1\n", + "Done: ADORA2A\n", + "Done: ADRB2\n", + "Done: AFAP1L2\n", + "Done: AFF1\n", + "Done: AGER\n", + "Done: AGO2\n", + "Done: AGTR1\n", + "Done: AHA2\n", + "Done: AHCYL1\n", + "Done: AHSA1\n", + "Done: AIFM1\n", + "Done: AIMP1\n", + "Done: AIMP2\n", + "Done: AIP\n", + "Done: AIRE\n", + "Done: AKAP1\n", + "Done: AKAP12\n", + "Done: AKAP13\n", + "Done: AKAP5\n", + "Done: AKT1\n", + "Done: AKT1S1\n", + "Done: ALDH1A1\n", + "Done: ALK\n", + "Done: AMOT\n", + "Done: AMOTL2\n", + "Done: AMPH\n", + "Done: ANPEP\n", + "Done: ANXA1\n", + "Done: ANXA2\n", + "Done: ANXA7\n", + "Done: AP2B1\n", + "Done: APAF1\n", + "Done: APBA2\n", + "Done: APBA3\n", + "Done: APBB1\n", + "Done: APC\n", + "Done: APEX1\n", + "Done: APPL1\n", + "Done: AQP2\n", + "Done: AQP5\n", + "Done: AR\n", + "Done: ARAP3\n", + "Done: ARFIP1\n", + "Done: ARHGAP17\n", + "Done: ARHGAP22\n", + "Done: ARHGAP33\n", + "Done: ARHGAP35\n", + "Done: ARHGDIA\n", + "Done: ARHGDIB\n", + "Done: ARHGEF2\n", + "Done: ARID3A\n", + "Done: ARID4A\n", + "Done: ARPP19\n", + "Done: ARRB1\n", + "Done: ARRB2\n", + "Done: ASAP1\n", + "Done: ASAP3\n", + "Done: ASF1A\n", + "Done: ATAD5\n", + "Done: ATF1\n", + "Done: ATF6\n", + "Done: ATG32\n", + "Done: ATG4B\n", + "Done: ATG9A\n", + "Done: ATM\n", + "Done: ATP5IF1\n", + "Done: ATR\n", + "Done: ATRIP\n", + "Done: ATXN1\n", + "Done: ATXN10\n", + "Done: AXL\n", + "Done: Akap200\n", + "Done: BABAM1\n", + "Done: BACE1\n", + "Done: BAD\n", + "Done: BAIAP2\n", + "Done: BAIAP2L1\n", + "Done: BAK1\n", + "Done: BANF1\n", + "Done: BAP1\n", + "Done: BBC3\n", + "Done: BCAR1\n", + "Done: BCL10\n", + "Done: BCL11B\n", + "Done: BCL2\n", + "Done: BCL2L1\n", + "Done: BCL2L11\n", + "Done: BCR\n", + "Done: BCR/ABL\n", + "Done: BECN1\n", + "Done: BEST1\n", + "Done: BIK\n", + "Done: BIN1\n", + "Done: BIRC5\n", + "Done: BLM\n", + "Done: BLNK\n", + "Done: BNIP3L\n", + "Done: BORA\n", + "Done: BRAF\n", + "Done: BRCA1\n", + "Done: BRCA2\n", + "Done: BRD4\n", + "Done: BRF1\n", + "Done: BRIP1\n", + "Done: BRMS1\n", + "Done: BTG1\n", + "Done: BTK\n", + "Done: BUB1\n", + "Done: BUB1B\n", + "Done: BUB3\n", + "Done: C16orf74\n", + "Done: C2orf88\n", + "Done: C3AR1\n", + "Done: CALD1\n", + "Done: CALM1\n", + "Done: CAMK2A\n", + "Done: CAMKK1\n", + "Done: CAMKK2\n", + "Done: CARD9\n", + "Done: CASP2\n", + "Done: CASP7\n", + "Done: CASP8\n", + "Done: CASR\n", + "Done: CASTOR1\n", + "Done: CAV1\n", + "Done: CAV2\n", + "Done: CAVIN1\n", + "Done: CBL\n", + "Done: CBLB\n", + "Done: CBLC\n", + "Done: CBX1\n", + "Done: CBX4\n", + "Done: CBY1\n", + "Done: CCAR1\n", + "Done: CCAR2\n", + "Done: CCDC106\n", + "Done: CCDC50\n", + "Done: CCDC6\n", + "Done: CCDC88A\n", + "Done: CCDC88C\n", + "Done: CCKBR\n", + "Done: CCND1\n", + "Done: CCND3\n", + "Done: CCNT1\n", + "Done: CCNY\n", + "Done: CCR7\n", + "Done: CD200R1\n", + "Done: CD226\n", + "Done: CD247\n", + "Done: CD274\n", + "Done: CD28\n", + "Done: CD300LF\n", + "Done: CD33\n", + "Done: CD36\n", + "Done: CD6\n", + "Done: CD93\n", + "Done: CDC20\n", + "Done: CDC25A\n", + "Done: CDC25B\n", + "Done: CDC25C\n", + "Done: CDC26\n", + "Done: CDC27\n", + "Done: CDC37\n", + "Done: CDC42\n", + "Done: CDC42EP4\n", + "Done: CDC73\n", + "Done: CDCA2\n", + "Done: CDCA5\n", + "Done: CDCA7\n", + "Done: CDCP1\n", + "Done: CDH1\n", + "Done: CDH2\n", + "Done: CDH5\n", + "Done: CDK10\n", + "Done: CDK16\n", + "Done: CDK2\n", + "Done: CDK5\n", + "Done: CDK5R1\n", + "Done: CDK5RAP2\n", + "Done: CDK6\n", + "Done: CDK9\n", + "Done: CDKN1A\n", + "Done: CDKN1B\n", + "Done: CDKN1C\n", + "Done: CDKN2A\n", + "Done: CDKN2D\n", + "Done: CDT1\n", + "Done: CEACAM3\n", + "Done: CEBPB\n", + "Done: CEBPD\n", + "Done: CEBPE\n", + "Done: CENPA\n", + "Done: CENPJ\n", + "Done: CENPU\n", + "Done: CEP131\n", + "Done: CEP192\n", + "Done: CEP55\n", + "Done: CERT1\n", + "Done: CETN1\n", + "Done: CETN2\n", + "Done: CFL1\n", + "Done: CFTR\n", + "Done: CGAS\n", + "Done: CHEK1\n", + "Done: CHEK2\n", + "Done: CHKA\n", + "Done: CIC\n", + "Done: CIITA\n", + "Done: CKMT1A\n", + "Done: CLASP2\n", + "Done: CLDN11\n", + "Done: CLDN16\n", + "Done: CLDN2\n", + "Done: CLDN4\n", + "Done: CLIC5\n", + "Done: CLIP1\n", + "Done: CLOCK\n", + "Done: CLSPN\n", + "Done: CLTC\n", + "Done: CNKSR1\n", + "Done: CNR1\n", + "Done: COP1\n", + "Done: CORO1A\n", + "Done: CORO1B\n", + "Done: CREB3L3\n", + "Done: CREBBP\n", + "Done: CRK\n", + "Done: CRTC2\n", + "Done: CRY2\n", + "Done: CRYAB\n", + "Done: CSF1R\n", + "Done: CSNK1A1\n", + "Done: CTBP1\n", + "Done: CTDP1\n", + "Done: CTLA4\n", + "Done: CTNNA1\n", + "Done: CTNNB1\n", + "Done: CTNND1\n", + "Done: CTPS1\n", + "Done: CTTN\n", + "Done: CUEDC2\n", + "Done: CXADR\n", + "Done: CXCR4\n", + "Done: CYBA\n", + "Done: CYLD\n", + "Done: Crb2\n", + "Done: DAAM1\n", + "Done: DAB1\n", + "Done: DAB2\n", + "Done: DACT1\n", + "Done: DAPK1\n", + "Done: DAXX\n", + "Done: DAZAP1\n", + "Done: DAZL\n", + "Done: DBN1\n", + "Done: DBNL\n", + "Done: DCC\n", + "Done: DCD\n", + "Done: DCK\n", + "Done: DCLRE1C\n", + "Done: DCTN6\n", + "Done: DCX\n", + "Done: DDB1\n", + "Done: DDR1\n", + "Done: DDX19B\n", + "Done: DDX3X\n", + "Done: DDX41\n", + "Done: DDX5\n", + "Done: DDX58\n", + "Done: DEF6\n", + "Done: DEK\n", + "Done: DEPTOR\n", + "Done: DIABLO\n", + "Done: DISC1\n", + "Done: DLG4\n", + "Done: DMAP1\n", + "Done: DNAJC5\n", + "Done: DNAJC6\n", + "Done: DNMT1\n", + "Done: DOC2B\n", + "Done: DOCK1\n", + "Done: DOCK8\n", + "Done: DOK1\n", + "Done: DPYSL2\n", + "Done: DPYSL5\n", + "Done: DRD1\n", + "Done: DRD3\n", + "Done: DTL\n", + "Done: DTNB\n", + "Done: DTYMK\n", + "Done: DUSP1\n", + "Done: DVL2\n", + "Done: DYNLL1\n", + "Done: DYNLT1\n", + "Done: DYRK1A\n", + "Done: Drpr\n", + "Done: E2F1\n", + "Done: ECD\n", + "Done: EDC3\n", + "Done: EEF2K\n", + "Done: EGFR\n", + "Done: EGLN2\n", + "Done: EHMT2\n", + "Done: EIF2AK2\n", + "Done: EIF2AK4\n", + "Done: EIF4A3\n", + "Done: EIF4B\n", + "Done: EIF4E\n", + "Done: EIF4EBP1\n", + "Done: EIF4G1\n", + "Done: EIF4G2\n", + "Done: ELAVL1\n", + "Done: ELK1\n", + "Done: ELMO1\n", + "Done: EMD\n", + "Done: EML4\n", + "Done: ENDOG\n", + "Done: ENSA\n", + "Done: EP300\n", + "Done: EPAS1\n", + "Done: EPHA2\n", + "Done: EPHB1\n", + "Done: EPHB3\n", + "Done: EPM2A\n", + "Done: EPRS1\n", + "Done: EPS8\n", + "Done: ERBB2\n", + "Done: ERBB3\n", + "Done: ERBB4\n", + "Done: ERCC6\n", + "Done: ERRFI1\n", + "Done: ESPL1\n", + "Done: ESR1\n", + "Done: ESR2\n", + "Done: ETS1\n", + "Done: ETV4\n", + "Done: EXO1\n", + "Done: EXOC7\n", + "Done: EZH2\n", + "Done: EZR\n", + "Done: F11R\n", + "Done: FADD\n", + "Done: FAF1\n", + "Done: FANCD2\n", + "Done: FANCG\n", + "Done: FBP1\n", + "Done: FBXO31\n", + "Done: FBXO4\n", + "Done: FBXW7\n", + "Done: FCRL6\n", + "Done: FEN1\n", + "Done: FERMT2\n", + "Done: FGF14\n", + "Done: FGFR1\n", + "Done: FGFR2\n", + "Done: FH\n", + "Done: FHIP2B\n", + "Done: FKBP5\n", + "Done: FKFBP\n", + "Done: FLII\n", + "Done: FLNA\n", + "Done: FLT3\n", + "Done: FLT4\n", + "Done: FNIP1\n", + "Done: FOS\n", + "Done: FOXL2\n", + "Done: FOXM1\n", + "Done: FOXN2\n", + "Done: FOXO1\n", + "Done: FOXO3\n", + "Done: FPR1\n", + "Done: FSCN1\n", + "Done: FTH1\n", + "Done: FUNDC1\n", + "Done: FUS\n", + "Done: FYB1\n", + "Done: FYB2\n", + "Done: FZD3\n", + "Done: FZR1\n", + "Done: G3BP1\n", + "Done: GAB1\n", + "Done: GAB2\n", + "Done: GABARAPL2\n", + "Done: GAREM1\n", + "Done: GAREM2\n", + "Done: GARS1\n", + "Done: GATA1\n", + "Done: GATA2\n", + "Done: GATA3\n", + "Done: GATAD2B\n", + "Done: GBF1\n", + "Done: GCH1\n", + "Done: GCM1\n", + "Done: GEM\n", + "Done: GFAP\n", + "Done: GFI1\n", + "Done: GGA1\n", + "Done: GIT1\n", + "Done: GJA1\n", + "Done: GLI1\n", + "Done: GLUD1\n", + "Done: GLUL\n", + "Done: GMFG\n", + "Done: GMNN\n", + "Done: GNA11\n", + "Done: GOLPH3\n", + "Done: GOT2\n", + "Done: GPR15\n", + "Done: GRB10\n", + "Done: GRB14\n", + "Done: GRB2\n", + "Done: GRB7\n", + "Done: GRIN2A\n", + "Done: GRIN2B\n", + "Done: GRK2\n", + "Done: GRN\n", + "Done: GSTA4\n", + "Done: GSTP1\n", + "Done: GTF2I\n", + "Done: GTF2IRD1\n", + "Done: GUCY1B1\n", + "Done: H1-2\n", + "Done: H1-4\n", + "Done: H2AC11\n", + "Done: H2AX\n", + "Done: H2AZ1\n", + "Done: H2BC3\n", + "Done: H3C1\n", + "Done: H4C1\n", + "Done: HCLS1\n", + "Done: HDAC2\n", + "Done: HDAC3\n", + "Done: HDAC4\n", + "Done: HDAC5\n", + "Done: HDAC6\n", + "Done: HERC2\n", + "Done: HIF1A\n", + "Done: HIPK2\n", + "Done: HJURP\n", + "Done: HMGN1\n", + "Done: HMOX1\n", + "Done: HNRNPA1\n", + "Done: HNRNPK\n", + "Done: HNRNPL\n", + "Done: HNRNPU\n", + "Done: HOXA11\n", + "Done: HRAS\n", + "Done: HRC\n", + "Done: HSD17B4\n", + "Done: HSF1\n", + "Done: HSF4\n", + "Done: HSP90AA1\n", + "Done: HSP90AB1\n", + "Done: HSPA1A\n", + "Done: HSPA5\n", + "Done: HSPB1\n", + "Done: HTR6\n", + "Done: HTT\n", + "Done: Hmr-1\n", + "Done: ID1\n", + "Done: ID3\n", + "Done: IDH1\n", + "Done: IDH2\n", + "Done: IFIH1\n", + "Done: IFNAR1\n", + "Done: IKBKG\n", + "Done: IL10RA\n", + "Done: IL22RA1\n", + "Done: IL4R\n", + "Done: IL6ST\n", + "Done: IL7R\n", + "Done: IL9R\n", + "Done: INCENP\n", + "Done: INSIG1\n", + "Done: INSIG2\n", + "Done: IQGAP1\n", + "Done: IQGAP2\n", + "Done: IRAK1\n", + "Done: IRAK4\n", + "Done: IRF3\n", + "Done: IRS1\n", + "Done: IRS4\n", + "Done: ISCU\n", + "Done: ITCH\n", + "Done: ITGB1\n", + "Done: ITGB2\n", + "Done: ITGB3BP\n", + "Done: ITGB4\n", + "Done: ITGB7\n", + "Done: ITPR1\n", + "Done: JAK2\n", + "Done: JAK3\n", + "Done: JUN\n", + "Done: JUNB\n", + "Done: JUP\n", + "Done: KAT6A\n", + "Done: KAT7\n", + "Done: KAT8\n", + "Done: KCNA2\n", + "Done: KCNH2\n", + "Done: KCNN4\n", + "Done: KCTD12\n", + "Done: KDM1A\n", + "Done: KDM3A\n", + "Done: KDM4C\n", + "Done: KDR\n", + "Done: KEAP1\n", + "Done: KHSRP\n", + "Done: KIF13B\n", + "Done: KIF22\n", + "Done: KIF23\n", + "Done: KIF2C\n", + "Done: KIF3A\n", + "Done: KIR2DL1\n", + "Done: KIT\n", + "Done: KLC2\n", + "Done: KLF10\n", + "Done: KLF4\n", + "Done: KLF5\n", + "Done: KLF8\n", + "Done: KLHL3\n", + "Done: KLRF1\n", + "Done: KMT2A\n", + "Done: KPNA2\n", + "Done: KPNA4\n", + "Done: KRAS\n", + "Done: KRT18\n", + "Done: KRT19\n", + "Done: KRT5\n", + "Done: Klp9\n", + "Done: L1CAM\n", + "Done: L3MBTL2\n", + "Done: LAIR1\n", + "Done: LARP6\n", + "Done: LARP7\n", + "Done: LASP1\n", + "Done: LCK\n", + "Done: LCP1\n", + "Done: LCP2\n", + "Done: LDHA\n", + "Done: LEF1\n", + "Done: LEMD3\n", + "Done: LEO1\n", + "Done: LGALS3\n", + "Done: LIG1\n", + "Done: LILRB2\n", + "Done: LIN52\n", + "Done: LMNA\n", + "Done: LMNB1\n", + "Done: LRP1\n", + "Done: LRP6\n", + "Done: LRRC4C\n", + "Done: LRRFIP2\n", + "Done: LRRK2\n", + "Done: LSR\n", + "Done: LY6G6F\n", + "Done: LZTS2\n", + "Done: MAD1L1\n", + "Done: MAD2L1\n", + "Done: MAD2L1BP\n", + "Done: MAF1\n", + "Done: MAFA\n", + "Done: MALT1\n", + "Done: MAML1\n", + "Done: MAP1LC3A\n", + "Done: MAP1LC3B\n", + "Done: MAP1LC3C\n", + "Done: MAP2\n", + "Done: MAP2K1\n", + "Done: MAP2K2\n", + "Done: MAP2K6\n", + "Done: MAP3K1\n", + "Done: MAP3K11\n", + "Done: MAP3K2\n", + "Done: MAP3K3\n", + "Done: MAP3K5\n", + "Done: MAP3K6\n", + "Done: MAP3K7\n", + "Done: MAP3K8\n", + "Done: MAP4K3\n", + "Done: MAPK1\n", + "Done: MAPK4\n", + "Done: MAPK6\n", + "Done: MAPK7\n", + "Done: MAPK8\n", + "Done: MAPK8IP1\n", + "Done: MAPRE1\n", + "Done: MAPRE3\n", + "Done: MARK2\n", + "Done: MARS1\n", + "Done: MAVS\n", + "Done: MCAM\n", + "Done: MCC\n", + "Done: MCF2\n", + "Done: MCL1\n", + "Done: MCM2\n", + "Done: MCM7\n", + "Done: MCPH1\n", + "Done: MCRIP1\n", + "Done: MDC1\n", + "Done: MDM2\n", + "Done: MDM4\n", + "Done: ME1\n", + "Done: MECOM\n", + "Done: MECP2\n", + "Done: MED1\n", + "Done: MED28\n", + "Done: MEF2C\n", + "Done: MEF2D\n", + "Done: MEFV\n", + "Done: MELK\n", + "Done: MET\n", + "Done: METTL14\n", + "Done: METTL3\n", + "Done: MEX3B\n", + "Done: MFF\n", + "Done: MFN2\n", + "Done: MIIP\n", + "Done: MIP\n", + "Done: MISP\n", + "Done: MLKL\n", + "Done: MLLT1\n", + "Done: MME\n", + "Done: MMP14\n", + "Done: MOB1A\n", + "Done: MORC2\n", + "Done: MPH1\n", + "Done: MPIG6B\n", + "Done: MPL\n", + "Done: MPLKIP\n", + "Done: MRE11\n", + "Done: MSN\n", + "Done: MST1R\n", + "Done: MTHFR\n", + "Done: MTOR\n", + "Done: MTSS1\n", + "Done: MTURN\n", + "Done: MUS81\n", + "Done: MVB12A\n", + "Done: MVP\n", + "Done: MYBL2\n", + "Done: MYC\n", + "Done: MYCN\n", + "Done: MYH9\n", + "Done: MYL12A\n", + "Done: MYL2\n", + "Done: MYOD1\n", + "Done: MZF1\n", + "Done: Mad\n", + "Done: Mtor\n", + "Done: NABP2\n", + "Done: NANOG\n", + "Done: NBN\n", + "Done: NCAPD3\n", + "Done: NCF1\n", + "Done: NCOA3\n", + "Done: NCOA6\n", + "Done: NDD1\n", + "Done: NDE1\n", + "Done: NDRG1\n", + "Done: NEDD1\n", + "Done: NEDD4L\n", + "Done: NEK7\n", + "Done: NEK9\n", + "Done: NELFE\n", + "Done: NF2\n", + "Done: NFAT5\n", + "Done: NFATC1\n", + "Done: NFATC2\n", + "Done: NFE2L2\n", + "Done: NFKB2\n", + "Done: NGFR\n", + "Done: NHEJ1\n", + "Done: NIBAN1\n", + "Done: NIBAN2\n", + "Done: NIFK\n", + "Done: NINL\n", + "Done: NKX3-1\n", + "Done: NLRP3\n", + "Done: NOLC1\n", + "Done: NOP53\n", + "Done: NOS3\n", + "Done: NOX4\n", + "Done: NOXA1\n", + "Done: NPHP1\n", + "Done: NPHS1\n", + "Done: NPM1\n", + "Done: NQO1\n", + "Done: NR1I2\n", + "Done: NR1I3\n", + "Done: NR3C1\n", + "Done: NR4A1\n", + "Done: NRAS\n", + "Done: NRBF2\n", + "Done: NRIP1\n", + "Done: NSD2\n", + "Done: NSF\n", + "Done: NSUN2\n", + "Done: NTRK1\n", + "Done: NUPR1\n", + "Done: OCLN\n", + "Done: OFD1\n", + "Done: OPTN\n", + "Done: OSBP2\n", + "Done: OSTF1\n", + "Done: OTULIN\n", + "Done: OXSR1\n", + "Done: P2RY1\n", + "Done: P4HB\n", + "Done: PA2G4\n", + "Done: PABIR1\n", + "Done: PACSIN1\n", + "Done: PACSIN2\n", + "Done: PAG1\n", + "Done: PAGE4\n", + "Done: PAK1\n", + "Done: PAK4\n", + "Done: PAK6\n", + "Done: PARD3\n", + "Done: PARD3B\n", + "Done: PARK7\n", + "Done: PARP1\n", + "Done: PARP10\n", + "Done: PARVA\n", + "Done: PBK\n", + "Done: PCGF2\n", + "Done: PCNA\n", + "Done: PCYT1A\n", + "Done: PDCD4\n", + "Done: PDCD6IP\n", + "Done: PDCL\n", + "Done: PDE3A\n", + "Done: PDE3B\n", + "Done: PDGFRA\n", + "Done: PDGFRB\n", + "Done: PDHA1\n", + "Done: PDP1\n", + "Done: PDPK1\n", + "Done: PDZK1\n", + "Done: PEAK1\n", + "Done: PEBP1\n", + "Done: PES1\n", + "Done: PEX14\n", + "Done: PEX5\n", + "Done: PFKFB2\n", + "Done: PFKP\n", + "Done: PFN1\n", + "Done: PGK1\n", + "Done: PGR\n", + "Done: PHB1\n", + "Done: PHB2\n", + "Done: PHF8\n", + "Done: PICK1\n", + "Done: PIDD1\n", + "Done: PIK3C3\n", + "Done: PIK3CG\n", + "Done: PIK3R1\n", + "Done: PIK3R2\n", + "Done: PIN1\n", + "Done: PIP5K1C\n", + "Done: PITPNC1\n", + "Done: PKM\n", + "Done: PKMYT1\n", + "Done: PKP1\n", + "Done: PKP2\n", + "Done: PKP3\n", + "Done: PLCG1\n", + "Done: PLEC\n", + "Done: PLEKHG2\n", + "Done: PLEKHG6\n", + "Done: PLK1\n", + "Done: PLN\n", + "Done: PLSCR1\n", + "Done: PLXNB1\n", + "Done: PMAIP1\n", + "Done: PML\n", + "Done: POLE\n", + "Done: POLL\n", + "Done: POLR2A\n", + "Done: POLR2M\n", + "Done: POU5F1\n", + "Done: PPARA\n", + "Done: PPARD\n", + "Done: PPIF\n", + "Done: PPP1R12A\n", + "Done: PPP1R12C\n", + "Done: PPP1R13L\n", + "Done: PPP1R16B\n", + "Done: PPP2CA\n", + "Done: PPP2R5C\n", + "Done: PRC1\n", + "Done: PRICKLE1\n", + "Done: PRKACA\n", + "Done: PRKAR1A\n", + "Done: PRKCD\n", + "Done: PRKCE\n", + "Done: PRKD1\n", + "Done: PRKD2\n", + "Done: PRKDC\n", + "Done: PRKN\n", + "Done: PRKRA\n", + "Done: PRLR\n", + "Done: PRMT7\n", + "Done: PROX1\n", + "Done: PSEN1\n", + "Done: PSEN2\n", + "Done: PSMD1\n", + "Done: PSMD2\n", + "Done: PSME3\n", + "Done: PTEN\n", + "Done: PTGES3\n", + "Done: PTK2\n", + "Done: PTK2B\n", + "Done: PTPN11\n", + "Done: PTPN12\n", + "Done: PTPN22\n", + "Done: PTPN6\n", + "Done: PTPRJ\n", + "Done: PTS\n", + "Done: PTTG1IP\n", + "Done: PXN\n", + "Done: Piwi\n", + "Done: Pop-1\n", + "Done: RAB11FIP5\n", + "Done: RAB1A\n", + "Done: RAB7A\n", + "Done: RAB8A\n", + "Done: RABEP1\n", + "Done: RAC1\n", + "Done: RACGAP1\n", + "Done: RACK1\n", + "Done: RAD51\n", + "Done: RAD52\n", + "Done: RAD9A\n", + "Done: RAF1\n", + "Done: RAG2\n", + "Done: RALGAPA2\n", + "Done: RAN\n", + "Done: RANGAP1\n", + "Done: RAP1A\n", + "Done: RAP1B\n", + "Done: RAP1GAP\n", + "Done: RAP1GAP2\n", + "Done: RAPGEF2\n", + "Done: RARA\n", + "Done: RB1\n", + "Done: RBBP5\n", + "Done: RBBP8\n", + "Done: RBL1\n", + "Done: RBL2\n", + "Done: RBM25\n", + "Done: RBM38\n", + "Done: RBM4\n", + "Done: RBM7\n", + "Done: RC3H2\n", + "Done: RCC1\n", + "Done: RCHY1\n", + "Done: RECQL4\n", + "Done: RELA\n", + "Done: RELB\n", + "Done: REM1\n", + "Done: REST\n", + "Done: RET\n", + "Done: RETREG1\n", + "Done: RGS18\n", + "Done: RGS5\n", + "Done: RGS7\n", + "Done: RHO\n", + "Done: RHOA\n", + "Done: RICTOR\n", + "Done: RIMS1\n", + "Done: RIN1\n", + "Done: RIPK1\n", + "Done: RIPK2\n", + "Done: RIPK3\n", + "Done: RMDN3\n", + "Done: RND3\n", + "Done: RNF187\n", + "Done: RNMT\n", + "Done: ROCK2\n", + "Done: RORA\n", + "Done: RPA1\n", + "Done: RPS10\n", + "Done: RPTOR\n", + "Done: RRM1\n", + "Done: RRM2\n", + "Done: RRN3\n", + "Done: RUNX1\n", + "Done: RUNX3\n", + "Done: RUVBL2\n", + "Done: RXRA\n", + "Done: S100A11\n", + "Done: SAFB\n", + "Done: SAMSN1\n", + "Done: SASH1\n", + "Done: SATB1\n", + "Done: SCN1A\n", + "Done: SCN5A\n", + "Done: SDC1\n", + "Done: SDC2\n", + "Done: SDC4\n", + "Done: SDCBP\n", + "Done: SEC23A\n", + "Done: SEC23B\n", + "Done: SEC63\n", + "Done: SECISBP2L\n", + "Done: SELL\n", + "Done: SEPTIN12\n", + "Done: SEPTIN7\n", + "Done: SERINC3\n", + "Done: SF3B2\n", + "Done: SFN\n", + "Done: SFPQ\n", + "Done: SGK3\n", + "Done: SGO1\n", + "Done: SGTA\n", + "Done: SH2D1B\n", + "Done: SH2D2A\n", + "Done: SH3BP2\n", + "Done: SH3BP4\n", + "Done: SH3GL1\n", + "Done: SH3GL2\n", + "Done: SH3KBP1\n", + "Done: SH3RF1\n", + "Done: SHCBP1\n", + "Done: SHOC2\n", + "Done: SIAH1\n", + "Done: SIGIRR\n", + "Done: SIK3\n", + "Done: SIRT1\n", + "Done: SIRT2\n", + "Done: SIRT7\n", + "Done: SIT1\n", + "Done: SKA3\n", + "Done: SKAP1\n", + "Done: SKP2\n", + "Done: SLC2A1\n", + "Done: SLC4A1\n", + "Done: SLC9A1\n", + "Done: SLC9A3R1\n", + "Done: SLC9A3R2\n", + "Done: SLD2\n", + "Done: SLITRK1\n", + "Done: SMAD1\n", + "Done: SMAD2\n", + "Done: SMAD3\n", + "Done: SMAD4\n", + "Done: SMAD7\n", + "Done: SMARCA4\n", + "Done: SMC1A\n", + "Done: SMG9\n", + "Done: SMN1\n", + "Done: SMURF2\n", + "Done: SNAI1\n", + "Done: SNAI2\n", + "Done: SNAP23\n", + "Done: SNAP25\n", + "Done: SNAP91\n", + "Done: SNAPIN\n", + "Done: SNCA\n", + "Done: SNCAIP\n", + "Done: SND1\n", + "Done: SNW1\n", + "Done: SNX27\n", + "Done: SNX5\n", + "Done: SNX8\n", + "Done: SOCS1\n", + "Done: SOCS3\n", + "Done: SOD1\n", + "Done: SORBS2\n", + "Done: SOS1\n", + "Done: SOX2\n", + "Done: SOX9\n", + "Done: SP1\n", + "Done: SPHK1\n", + "Done: SPI1\n", + "Done: SPOP\n", + "Done: SPRED1\n", + "Done: SPRR2B\n", + "Done: SPRY2\n", + "Done: SPSB1\n", + "Done: SQSTM1\n", + "Done: SRC\n", + "Done: SREBF1\n", + "Done: SRPK2\n", + "Done: SRY\n", + "Done: SSH1\n", + "Done: SSTR2\n", + "Done: STAP2\n", + "Done: STAR\n", + "Done: STARD3\n", + "Done: STAT1\n", + "Done: STAT2\n", + "Done: STAT3\n", + "Done: STAT4\n", + "Done: STAT6\n", + "Done: STIL\n", + "Done: STIM1\n", + "Done: STING1\n", + "Done: STK11\n", + "Done: STK3\n", + "Done: STK38\n", + "Done: STK4\n", + "Done: STMN1\n", + "Done: STX17\n", + "Done: STX1A\n", + "Done: STXBP2\n", + "Done: STYK1\n", + "Done: SUFU\n", + "Done: SULT4A1\n", + "Done: SUZ12\n", + "Done: SVIL\n", + "Done: SWAP70\n", + "Done: SYK\n", + "Done: Slob\n", + "Done: TACSTD2\n", + "Done: TAGAP\n", + "Done: TAGLN\n", + "Done: TAGLN2\n", + "Done: TAL1\n", + "Done: TARBP2\n", + "Done: TARDBP\n", + "Done: TBC1D1\n", + "Done: TBC1D4\n", + "Done: TBK1\n", + "Done: TBL1X\n", + "Done: TCF21\n", + "Done: TCF3\n", + "Done: TCOF1\n", + "Done: TDP1\n", + "Done: TELO2\n", + "Done: TERF1\n", + "Done: TERF2\n", + "Done: TERT\n", + "Done: TET2\n", + "Done: TFEB\n", + "Done: TGFB1I1\n", + "Done: TGFBR1\n", + "Done: TGFBR2\n", + "Done: TGFBR3\n", + "Done: TGM2\n", + "Done: TH\n", + "Done: THRB\n", + "Done: TIAM1\n", + "Done: TICAM1\n", + "Done: TIGIT\n", + "Done: TIMELESS\n", + "Done: TIMP2\n", + "Done: TJP1\n", + "Done: TK1\n", + "Done: TNFAIP1\n", + "Done: TNFAIP8L2\n", + "Done: TNFRSF1A\n", + "Done: TNK2\n", + "Done: TNNI3\n", + "Done: TOB2\n", + "Done: TOM1L1\n", + "Done: TOP1\n", + "Done: TOP2A\n", + "Done: TOPBP1\n", + "Done: TOPORS\n", + "Done: TP53\n", + "Done: TP53BP1\n", + "Done: TP73\n", + "Done: TPH2\n", + "Done: TPK1\n", + "Done: TPS5\n", + "Done: TPT1\n", + "Done: TRADD\n", + "Done: TRAF2\n", + "Done: TRAF3\n", + "Done: TRAPPC6A\n", + "Done: TRIM11\n", + "Done: TRIM14\n", + "Done: TRIM21\n", + "Done: TRIM24\n", + "Done: TRIM28\n", + "Done: TRIM29\n", + "Done: TRIM32\n", + "Done: TRIM33\n", + "Done: TRIM59\n", + "Done: TRIP10\n", + "Done: TRPC4\n", + "Done: TRPV4\n", + "Done: TSC1\n", + "Done: TSC2\n", + "Done: TTI1\n", + "Done: TTK\n", + "Done: TUBA1A\n", + "Done: UBE2I\n", + "Done: UBE2J1\n", + "Done: UBTF\n", + "Done: UFD1\n", + "Done: UFL1\n", + "Done: UHRF1\n", + "Done: ULK1\n", + "Done: ULK2\n", + "Done: UNG\n", + "Done: UPF1\n", + "Done: URI1\n", + "Done: USP13\n", + "Done: USP15\n", + "Done: USP16\n", + "Done: USP20\n", + "Done: USP21\n", + "Done: USP4\n", + "Done: USP8\n", + "Done: UTRN\n", + "Done: UVRAG\n", + "Done: VASP\n", + "Done: VAV1\n", + "Done: VCP\n", + "Done: VCPIP1\n", + "Done: VDR\n", + "Done: VGLL1\n", + "Done: VHL\n", + "Done: VIM\n", + "Done: VRK3\n", + "Done: WAS\n", + "Done: WASF1\n", + "Done: WDHD1\n", + "Done: WDR62\n", + "Done: WEE1\n", + "Done: WIPF1\n", + "Done: WNK1\n", + "Done: WRAP53\n", + "Done: WRN\n", + "Done: WWOX\n", + "Done: WWP2\n", + "Done: WWTR1\n", + "Done: XIAP\n", + "Done: XPA\n", + "Done: XRCC1\n", + "Done: XRCC4\n", + "Done: XRCC6\n", + "Done: YAP1\n", + "Done: YWHAH\n", + "Done: YWHAZ\n", + "Done: Yki\n", + "Done: ZAP70\n", + "Done: ZBTB7A\n", + "Done: ZEB2\n", + "Done: ZFP36L1\n", + "Done: ZMYM2\n", + "Done: ZNF281\n", + "Done: ZNF282\n", + "Done: ZNF76\n", + "Done: ZNRF2\n", + "Done: ZWINT\n", + "Done: ZYX\n" + ] + } + ], + "source": [ + "CSV_PATH = \"../data/ptmint_dataset.csv\"\n", + "\n", + "df = pd.read_csv(CSV_PATH)\n", + "genes = sorted(set(df[\"Gene\"].dropna().astype(str)))\n", + "\n", + "header = [\n", + "\"Organism\",\"Gene\",\"Uniprot\",\"PTM\",\"Site\",\"AA\",\"Int_uniprot\",\"Int_gene\",\n", + "\"Effect\",\"Method\",\"Disease\",\"Co_localized\",\"PMID\",\"Complex\",\"Origin\",\n", + "\"Confidence\",\"PDBRES\",\"Score\",\"Interface\",\"Domain\"\n", + "]\n", + "\n", + "os.makedirs(\"../data/protein_features\", exist_ok=True)\n", + "\n", + "with open(\"../data/ptmint_iufeatures.txt\", \"w\") as out:\n", + "\n", + " out.write(\"\\t\".join(header) + \"\\n\")\n", + "\n", + " for gene in genes:\n", + "\n", + " # ---- scrape interaction table ----\n", + " url = f\"https://ptmint.sjtu.edu.cn/Search/Phos/{gene}\"\n", + " r = requests.get(url)\n", + "\n", + " soup = BeautifulSoup(r.text, \"html.parser\")\n", + " table = soup.find(\"table\", {\"id\": \"data\"})\n", + "\n", + " if table is not None:\n", + " for tr in table.find_all(\"tr\")[1:]:\n", + " cols = [td.get_text(strip=True) for td in tr.find_all(\"td\")]\n", + " out.write(\"\\t\".join(cols) + \"\\n\")\n", + "\n", + " # ---- download protein feature csv ----\n", + " feat_url = f\"https://ptmint.sjtu.edu.cn/data/{gene}_protein_features.csv\"\n", + " feat_file = f\"../data/protein_features/{gene}_protein_features.csv\"\n", + "\n", + " rf = requests.get(feat_url)\n", + " if rf.status_code == 200:\n", + " with open(feat_file, \"wb\") as f:\n", + " f.write(rf.content)\n", + "\n", + " print(\"Done:\", gene)\n", + "\n", + " time.sleep(0.3)\n", + "\n", + "input_file = \"../data/ptmint_iufeatures.txt\"\n", + "output_file = \"../data/ptmint_iufeatures.csv\"\n", + "df = pd.read_csv(input_file, sep=\"\\t\")\n", + "df.to_csv(output_file, index=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### 3. Get additional information (sequence strings, unify with interface data)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import os\n", + "import pandas as pd\n", + "from Bio.PDB import PDBParser, PPBuilder\n", + "\n", + "pd.set_option('display.max_columns', None)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Interacting chain names and sequences" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "PDB_DIR = \"../data/ProteinStructures/Complexes\"\n", + "STRUCT_DF = \"../data/ptmint_iufeatures.csv\"\n", + "parser = PDBParser(QUIET=True)\n", + "ppb = PPBuilder()\n", + "\n", + "df = pd.read_csv(\"/nfs/turbo/umms-ajitj/PTMint/data/ptmint_iufeatures.csv\")\n", + "\n", + "def get_chain_sequence_from_structure(structure, chain_id):\n", + " model = structure[0]\n", + " if chain_id not in model:\n", + " return \"\"\n", + " chain = model[chain_id]\n", + " peptides = ppb.build_peptides(chain)\n", + " if not peptides:\n", + " return \"\"\n", + " return \"\".join(str(pp.get_sequence()) for pp in peptides)\n", + "\n", + "def get_two_chain_ids(pdb_path):\n", + " \"\"\"Return the two chain IDs in model 0. If not exactly 2, return what exists.\"\"\"\n", + " structure = parser.get_structure(\"complex\", pdb_path)\n", + " model = structure[0]\n", + " chain_ids = [c.id for c in model.get_chains()]\n", + " return structure, chain_ids\n", + "\n", + "def extract_two_chain_seqs(pdb_path):\n", + " \"\"\"\n", + " Returns:\n", + " (chain1_id, seq1, chain2_id, seq2)\n", + " Assumes exactly 2 chains, but doesn't crash if not.\n", + " \"\"\"\n", + " structure, chain_ids = get_two_chain_ids(pdb_path)\n", + "\n", + " if len(chain_ids) < 2:\n", + " c1 = chain_ids[0] if len(chain_ids) == 1 else \"\"\n", + " s1 = get_chain_sequence_from_structure(structure, c1) if c1 else \"\"\n", + " return c1, s1, \"\", \"\"\n", + "\n", + " if len(chain_ids) > 2:\n", + " # PTMint says it should be exactly 2; fail loudly so you notice bad files.\n", + " raise ValueError(f\"{pdb_path} has {len(chain_ids)} chains: {chain_ids} (expected exactly 2)\")\n", + "\n", + " c1, c2 = chain_ids[0], chain_ids[1]\n", + " s1 = get_chain_sequence_from_structure(structure, c1)\n", + " s2 = get_chain_sequence_from_structure(structure, c2)\n", + " return c1, s1, c2, s2\n", + "\n", + "def add_interactor_sequences(df):\n", + " df = df.copy()\n", + " df[\"pdb_path\"] = df[\"Complex\"].astype(str).str.replace(\".pdb\", \"\", regex=False) \\\n", + " .apply(lambda x: os.path.join(PDB_DIR, f\"{x}.pdb\"))\n", + "\n", + " out = df[\"pdb_path\"].apply(extract_two_chain_seqs)\n", + "\n", + " df[\"Interactor_chain_1\"] = out.apply(lambda t: t[0])\n", + " df[\"Interactor_1_seq\"] = out.apply(lambda t: t[1])\n", + " df[\"Interactor_chain_2\"] = out.apply(lambda t: t[2])\n", + " df[\"Interactor_2_seq\"] = out.apply(lambda t: t[3])\n", + "\n", + " return df\n", + "\n", + "df = add_interactor_sequences(df)\n", + "df.drop(columns=[\"pdb_path\"], inplace=True)\n", + "\n", + "output_file = \"../data/ptmint_with_seqs.csv\"\n", + "df.to_csv(output_file, index=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Interface residue numbers and names" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "output_file = \"../data/ptmint_with_seqs.csv\"\n", + "df = pd.read_csv(output_file)\n", + "\n", + "# 1) Read interface residues\n", + "iface = pd.read_csv(\n", + " \"../data/ProteinStructures/complex_interface.csv\"\n", + ")\n", + "\n", + "aa3_to_aa1 = {\n", + " \"ALA\":\"A\",\"ARG\":\"R\",\"ASN\":\"N\",\"ASP\":\"D\",\"CYS\":\"C\",\n", + " \"GLN\":\"Q\",\"GLU\":\"E\",\"GLY\":\"G\",\"HIS\":\"H\",\"ILE\":\"I\",\n", + " \"LEU\":\"L\",\"LYS\":\"K\",\"MET\":\"M\",\"PHE\":\"F\",\"PRO\":\"P\",\n", + " \"SER\":\"S\",\"THR\":\"T\",\"TRP\":\"W\",\"TYR\":\"Y\",\"VAL\":\"V\"\n", + "}\n", + "\n", + "iface[\"AA1\"] = iface[\"AA\"].map(aa3_to_aa1).fillna(\"X\")\n", + "\n", + "# ------------------------------------------------\n", + "# 2) interface_sites_num → {chain: \"site1,site2,...\"}\n", + "# ------------------------------------------------\n", + "\n", + "sites_agg = (\n", + " iface.groupby([\"Complex\", \"Chain\"])[\"Site\"]\n", + " .apply(lambda s: \",\".join(map(str, s.tolist())))\n", + " .reset_index(name=\"sites\")\n", + ")\n", + "\n", + "sites_dict = (\n", + " sites_agg.groupby(\"Complex\")\n", + " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"sites\"])))\n", + " .to_dict()\n", + ")\n", + "\n", + "df[\"interface_sites_num\"] = df[\"Complex\"].map(sites_dict).apply(\n", + " lambda x: x if isinstance(x, dict) else {}\n", + ")\n", + "\n", + "# ------------------------------------------------\n", + "# 3) interface_sequence_dict → {chain: \"A,S,T,...\"}\n", + "# ------------------------------------------------\n", + "\n", + "seq_agg = (\n", + " iface.groupby([\"Complex\", \"Chain\"])[\"AA1\"]\n", + " .apply(lambda s: \",\".join(s.tolist()))\n", + " .reset_index(name=\"seqs\")\n", + ")\n", + "\n", + "seq_dict = (\n", + " seq_agg.groupby(\"Complex\")\n", + " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"seqs\"])))\n", + " .to_dict()\n", + ")\n", + "\n", + "df[\"interface_sequence_dict\"] = df[\"Complex\"].map(seq_dict).apply(\n", + " lambda x: x if isinstance(x, dict) else {}\n", + ")\n", + "\n", + "df_original = pd.read_csv(\"../data/ptmint_dataset.csv\")\n", + "df.to_csv(\"../intermediate/ptmint_interm.csv\", index=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### 4. Extract sequence information from complexes PDBs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "from pathlib import Path\n", + "from Bio.PDB import PDBParser, PPBuilder\n", + "import time\n", + "import requests\n", + "import pandas as pd" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Wrote 2960 rows -> ../data/complex_chain_seqs.csv\n" + ] + } + ], + "source": [ + "PDB_DIR = Path(\"../data/ProteinStructures/Complexes\")\n", + "OUT_CSV = Path(\"../data/complex_chain_seqs.csv\")\n", + "\n", + "parser = PDBParser(QUIET=True)\n", + "ppb = PPBuilder()\n", + "\n", + "def get_chain_sequence_from_structure(structure, chain_id: str) -> str:\n", + " model = structure[0]\n", + " if chain_id not in model:\n", + " return \"\"\n", + " chain = model[chain_id]\n", + " peptides = ppb.build_peptides(chain)\n", + " if not peptides:\n", + " return \"\"\n", + " # Concatenate peptide fragments (handles chain breaks)\n", + " return \"\".join(str(pp.get_sequence()) for pp in peptides)\n", + "\n", + "def extract_two_chain_seqs(pdb_path: Path):\n", + " \"\"\"\n", + " Returns (c1, s1, c2, s2).\n", + " Raises if more than 2 chains (so you notice unexpected files).\n", + " \"\"\"\n", + " structure = parser.get_structure(pdb_path.stem, str(pdb_path))\n", + " model = structure[0]\n", + " chain_ids = [c.id for c in model.get_chains()]\n", + "\n", + " if len(chain_ids) == 0:\n", + " return \"\", \"\", \"\", \"\"\n", + " if len(chain_ids) == 1:\n", + " c1 = chain_ids[0]\n", + " s1 = get_chain_sequence_from_structure(structure, c1)\n", + " return c1, s1, \"\", \"\"\n", + " if len(chain_ids) > 2:\n", + " raise ValueError(f\"{pdb_path} has {len(chain_ids)} chains: {chain_ids} (expected exactly 2)\")\n", + "\n", + " c1, c2 = chain_ids[0], chain_ids[1]\n", + " s1 = get_chain_sequence_from_structure(structure, c1)\n", + " s2 = get_chain_sequence_from_structure(structure, c2)\n", + " return c1, s1, c2, s2\n", + "\n", + "rows = []\n", + "errors = []\n", + "\n", + "for pdb_path in sorted(PDB_DIR.glob(\"*.pdb\")):\n", + " complex_name = pdb_path.name # keep .pdb in Complex; change to pdb_path.stem if you want no extension\n", + " try:\n", + " c1, s1, c2, s2 = extract_two_chain_seqs(pdb_path)\n", + " rows.append({\n", + " \"Complex\": complex_name,\n", + " \"Interactor_chain_1\": c1,\n", + " \"Interactor_1_seq\": s1,\n", + " \"Interactor_chain_2\": c2,\n", + " \"Interactor_2_seq\": s2,\n", + " })\n", + " except Exception as e:\n", + " errors.append((pdb_path.name, str(e)))\n", + "\n", + "df_out = pd.DataFrame(rows, columns=[\n", + " \"Complex\",\n", + " \"Interactor_chain_1\", \"Interactor_1_seq\",\n", + " \"Interactor_chain_2\", \"Interactor_2_seq\",\n", + "])\n", + "\n", + "OUT_CSV.parent.mkdir(parents=True, exist_ok=True)\n", + "df_out.to_csv(OUT_CSV, index=False)\n", + "\n", + "print(f\"Wrote {len(df_out)} rows -> {OUT_CSV}\")\n", + "if errors:\n", + " print(\"\\nFiles with errors:\")\n", + " for fn, msg in errors:\n", + " print(f\" {fn}: {msg}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Wrote: ../intermediate/ptmint_merged_with_uniprot_seqs.csv (rows=5156)\n" + ] + } + ], + "source": [ + "df_original = pd.read_csv(\"../data/ptmint_dataset.csv\")\n", + "df_original = df_original.rename(columns={\"Sequence window(-5,+5)\": \"SequenceWindow\"})\n", + "df_new = pd.read_csv(\"../intermediate/ptmint_interm.csv\").drop_duplicates()\n", + "\n", + "merge_keys = [\n", + " 'Organism', 'Gene', 'Uniprot', 'PTM', 'Site', 'AA',\n", + " 'Int_uniprot', 'Int_gene', 'Effect', 'Method', 'Disease', 'PMID'\n", + "]\n", + "\n", + "df2 = df_original.merge(\n", + " df_new,\n", + " on=merge_keys,\n", + " how='left',\n", + ")\n", + "\n", + "df2.to_csv(\"../intermediate/ptmint_merged.csv\", index=False)\n", + "\n", + "\n", + "INPUT_CSV = \"../intermediate/ptmint_merged.csv\"\n", + "OUTPUT_CSV = \"../intermediate/ptmint_merged_with_uniprot_seqs.csv\"\n", + "\n", + "UNIPROT_FASTA_URL = \"https://rest.uniprot.org/uniprotkb/{}.fasta\"\n", + "\n", + "SLEEP_BETWEEN_REbQUESTS_SEC = 0.05\n", + "TIMEOUT_SEC = 30\n", + "\n", + "session = requests.Session()\n", + "\n", + "def fasta_to_sequence(fasta_text: str) -> str:\n", + " \"\"\"Convert FASTA text into a single continuous AA sequence string.\"\"\"\n", + " if not fasta_text:\n", + " return \"\"\n", + " lines = [ln.strip() for ln in fasta_text.splitlines() if ln.strip()]\n", + " if not lines:\n", + " return \"\"\n", + " # drop header lines starting with '>'\n", + " seq_lines = [ln for ln in lines if not ln.startswith(\">\")]\n", + " return \"\".join(seq_lines).replace(\" \", \"\")\n", + "\n", + "def fetch_uniprot_sequence(uniprot_id: str) -> str:\n", + " \"\"\"Download FASTA from UniProt and return the AA sequence; return '' on failure.\"\"\"\n", + " if uniprot_id is None:\n", + " return \"\"\n", + " uniprot_id = str(uniprot_id).strip()\n", + " if uniprot_id == \"\" or uniprot_id.lower() in {\"nan\", \"none\"}:\n", + " return \"\"\n", + "\n", + " url = UNIPROT_FASTA_URL.format(uniprot_id)\n", + "\n", + " try:\n", + " r = session.get(url, timeout=TIMEOUT_SEC)\n", + " if r.status_code != 200:\n", + " return \"\"\n", + " return fasta_to_sequence(r.text)\n", + " except requests.RequestException:\n", + " return \"\"\n", + "\n", + "def add_sequences(df: pd.DataFrame) -> pd.DataFrame:\n", + " df = df.copy()\n", + "\n", + " # Cache to avoid repeated downloads\n", + " cache = {}\n", + "\n", + " def cached_get(acc):\n", + " acc_str = \"\" if pd.isna(acc) else str(acc).strip()\n", + " if acc_str == \"\" or acc_str.lower() in {\"nan\", \"none\"}:\n", + " return \"\"\n", + " if acc_str in cache:\n", + " return cache[acc_str]\n", + " seq = fetch_uniprot_sequence(acc_str)\n", + " cache[acc_str] = seq\n", + " time.sleep(SLEEP_BETWEEN_REQUESTS_SEC)\n", + " return seq\n", + "\n", + " # Create / overwrite columns\n", + " df[\"Gene_sequence\"] = df[\"Uniprot\"].apply(cached_get)\n", + " df[\"Int_gene_sequence\"] = df[\"Int_uniprot\"].apply(cached_get)\n", + "\n", + " return df\n", + "\n", + "df = pd.read_csv(INPUT_CSV)\n", + "\n", + "df2 = add_sequences(df)\n", + "\n", + "df2.to_csv(OUTPUT_CSV, index=False)\n", + "print(f\"Wrote: {OUTPUT_CSV} (rows={len(df2)})\")" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Exact matches: 4376 / 5156\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "\n", + "df_uniprot = pd.read_csv(\"../intermediate/ptmint_merged_with_uniprot_seqs.csv\")\n", + "df_complex = pd.read_csv(\"../data/complex_chain_seqs.csv\")\n", + "\n", + "# --- build a \"normalized\" key so chain order doesn't matter ---\n", + "def make_key(a, b):\n", + " # treat (a,b) same as (b,a)\n", + " return (a, b) if a <= b else (b, a)\n", + "\n", + "df_u = df_uniprot.copy()\n", + "df_c = df_complex.copy()\n", + "\n", + "df_u[\"seqA\"] = df_u[\"Gene_sequence\"].fillna(\"\")\n", + "df_u[\"seqB\"] = df_u[\"Int_gene_sequence\"].fillna(\"\")\n", + "df_c[\"seq1\"] = df_c[\"Interactor_1_seq\"].fillna(\"\")\n", + "df_c[\"seq2\"] = df_c[\"Interactor_2_seq\"].fillna(\"\")\n", + "\n", + "# optional: strip whitespace/newlines, common in fasta-like strings\n", + "for col in [\"seqA\",\"seqB\"]:\n", + " df_u[col] = df_u[col].str.replace(r\"\\s+\", \"\", regex=True)\n", + "for col in [\"seq1\",\"seq2\"]:\n", + " df_c[col] = df_c[col].str.replace(r\"\\s+\", \"\", regex=True)\n", + "\n", + "df_u[[\"k1\",\"k2\"]] = df_u.apply(lambda r: pd.Series(make_key(r[\"seqA\"], r[\"seqB\"])), axis=1)\n", + "df_c[[\"k1\",\"k2\"]] = df_c.apply(lambda r: pd.Series(make_key(r[\"seq1\"], r[\"seq2\"])), axis=1)\n", + "\n", + "# If df_complex has duplicates for the same (k1,k2), decide how to handle:\n", + "# e.g., keep first (or you can keep all and do one-to-many)\n", + "df_c_dedup = df_c.drop_duplicates(subset=[\"k1\",\"k2\"], keep=\"first\")\n", + "\n", + "df_exact = df_u.merge(\n", + " df_c_dedup[[\"Complex\",\"Interactor_chain_1\",\"Interactor_1_seq\",\"Interactor_chain_2\",\"Interactor_2_seq\",\"k1\",\"k2\"]],\n", + " on=[\"k1\",\"k2\"],\n", + " how=\"left\",\n", + " suffixes=(\"\", \"_from_complex\")\n", + ")\n", + "\n", + "exact_hit_mask = df_exact[\"Complex_from_complex\"].notna()\n", + "print(\"Exact matches:\", exact_hit_mask.sum(), \" / \", len(df_exact))" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffect...seqAseqBk1k2Complex_from_complexInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexComplex_from_complex_clean
112HumanAKT1S1Q96B36Phos183SQQYAKsLPVSVQ8N122RPTORInhibit...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132.pdbAMASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...BMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132
113HumanAKT1S1Q96B36Phos183SQQYAKsLPVSVQ8N122RPTORInhibit...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132.pdbAMASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY...BMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA...Complex3132
250HumanATG4BQ9Y4P1Phos316SAELDPsIAVGFQ9GZQ8MAP1LC3BInhibit...MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV...MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV...MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV...MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV...Complex3327.pdbAMPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV...BMDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV...Complex3327
667HumanCDH1P12830Phos790TNDVAPtLMSVPP35222CTNNB1Inhibit...MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL...Complex1370_1.pdbAMGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL...BMATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...Complex1370_1
671HumanCDH5P33151Phos731YDTLHIyGYEGSP35222CTNNB1Inhibit...MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK...Complex1357_1.pdbAMQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK...BMATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL...Complex1357_1
..................................................................
1749HumanERBB4Q15303Phos1202YKAEDEyVNEPLP43405SYKEnhance...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...Complex2614_1.pdbAMKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...BMASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...Complex2614_1
1751HumanERBB4Q15303Phos1202YKAEDEyVNEPLP43405SYKEnhance...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...Complex2614_1.pdbAMKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...BMASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...Complex2614_1
1752HumanERBB4Q15303Phos1202YKAEDEyVNEPLP43405SYKEnhance...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...Complex2614_1.pdbAMKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY...BMASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN...Complex2614_1
1791HumanEZH2Q15910Phos311TYKRKNtETALDQ15022SUZ12Inhibit...MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR...MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC...MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC...MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR...Complex2565.pdbAMAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC...BMGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR...Complex2565
4523HumanSTK11Q15831Phos307SQIRQHsWFRKKQ7RTN6STRADAEnhance...MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI...MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS...MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI...MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS...Complex2687.pdbAMEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI...BMSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS...Complex2687
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396 rows × 41 columns

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" + ], + "text/plain": [ + " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", + "112 Human AKT1S1 Q96B36 Phos 183 S QQYAKsLPVSV Q8N122 \n", + "113 Human AKT1S1 Q96B36 Phos 183 S QQYAKsLPVSV Q8N122 \n", + "250 Human ATG4B Q9Y4P1 Phos 316 S AELDPsIAVGF Q9GZQ8 \n", + "667 Human CDH1 P12830 Phos 790 T NDVAPtLMSVP P35222 \n", + "671 Human CDH5 P33151 Phos 731 Y DTLHIyGYEGS P35222 \n", + "... ... ... ... ... ... .. ... ... \n", + "1749 Human ERBB4 Q15303 Phos 1202 Y KAEDEyVNEPL P43405 \n", + "1751 Human ERBB4 Q15303 Phos 1202 Y KAEDEyVNEPL P43405 \n", + "1752 Human ERBB4 Q15303 Phos 1202 Y KAEDEyVNEPL P43405 \n", + "1791 Human EZH2 Q15910 Phos 311 T YKRKNtETALD Q15022 \n", + "4523 Human STK11 Q15831 Phos 307 S QIRQHsWFRKK Q7RTN6 \n", + "\n", + " Int_gene Effect ... \\\n", + "112 RPTOR Inhibit ... \n", + "113 RPTOR Inhibit ... \n", + "250 MAP1LC3B Inhibit ... \n", + "667 CTNNB1 Inhibit ... \n", + "671 CTNNB1 Inhibit ... \n", + "... ... ... ... \n", + "1749 SYK Enhance ... \n", + "1751 SYK Enhance ... \n", + "1752 SYK Enhance ... \n", + "1791 SUZ12 Inhibit ... \n", + "4523 STRADA Enhance ... \n", + "\n", + " seqA \\\n", + "112 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", + "113 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", + "250 MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV... \n", + "667 MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL... \n", + "671 MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK... \n", + "... ... \n", + "1749 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", + "1751 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", + "1752 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", + "1791 MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR... \n", + "4523 MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI... \n", + "\n", + " seqB \\\n", + "112 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", + "113 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", + "250 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV... \n", + "667 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", + "671 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", + "... ... \n", + "1749 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1751 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1752 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1791 MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC... \n", + "4523 MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS... \n", + "\n", + " k1 \\\n", + "112 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", + "113 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", + "250 MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV... \n", + "667 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", + "671 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", + "... ... \n", + "1749 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1751 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1752 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1791 MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC... \n", + "4523 MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI... \n", + "\n", + " k2 Complex_from_complex \\\n", + "112 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... Complex3132.pdb \n", + "113 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... Complex3132.pdb \n", + "250 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV... Complex3327.pdb \n", + "667 MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL... Complex1370_1.pdb \n", + "671 MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK... Complex1357_1.pdb \n", + "... ... ... \n", + "1749 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... Complex2614_1.pdb \n", + "1751 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... Complex2614_1.pdb \n", + "1752 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... Complex2614_1.pdb \n", + "1791 MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR... Complex2565.pdb \n", + "4523 MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS... Complex2687.pdb \n", + "\n", + " Interactor_chain_1_from_complex \\\n", + "112 A \n", + "113 A \n", + "250 A \n", + "667 A \n", + "671 A \n", + "... ... \n", + "1749 A \n", + "1751 A \n", + "1752 A \n", + "1791 A \n", + "4523 A \n", + "\n", + " Interactor_1_seq_from_complex \\\n", + "112 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", + "113 MASGRPEELWEAVVGAAERFRARTGTELVLLTAAPPPPPRPGPCAY... \n", + "250 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPV... \n", + "667 MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHL... \n", + "671 MQRLMMLLATSGACLGLLAVAAVAAAGANPAQRDTHSLLPTHRRQK... \n", + "... ... \n", + "1749 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", + "1751 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", + "1752 MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQY... \n", + "1791 MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSC... \n", + "4523 MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLI... \n", + "\n", + " Interactor_chain_2_from_complex \\\n", + "112 B \n", + "113 B \n", + "250 B \n", + "667 B \n", + "671 B \n", + "... ... \n", + "1749 B \n", + "1751 B \n", + "1752 B \n", + "1791 B \n", + "4523 B \n", + "\n", + " Interactor_2_seq_from_complex \\\n", + "112 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", + "113 MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLA... \n", + "250 MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDV... \n", + "667 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", + "671 MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSL... \n", + "... ... \n", + "1749 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1751 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1752 MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRN... \n", + "1791 MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNR... \n", + "4523 MSFLVSKPERIRRWVSEKFIVEGLRDLELFGEQPPGDTRRKTNDAS... \n", + "\n", + " Complex_from_complex_clean \n", + "112 Complex3132 \n", + "113 Complex3132 \n", + "250 Complex3327 \n", + "667 Complex1370_1 \n", + "671 Complex1357_1 \n", + "... ... \n", + "1749 Complex2614_1 \n", + "1751 Complex2614_1 \n", + "1752 Complex2614_1 \n", + "1791 Complex2565 \n", + "4523 Complex2687 \n", + "\n", + "[396 rows x 41 columns]" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "#Check for differences between complex ID from website and obtained through alignment\n", + "df_exact[\"Complex_from_complex_clean\"] = (\n", + " df_exact[\"Complex_from_complex\"]\n", + " .str.replace(\".pdb\", \"\", regex=False)\n", + ")\n", + "\n", + "df_exact[\n", + " df_exact[\"Complex\"].notna() &\n", + " df_exact[\"Complex_from_complex_clean\"].notna() &\n", + " (df_exact[\"Complex\"] != \"\") &\n", + " (df_exact[\"Complex_from_complex_clean\"] != \"\") &\n", + " (df_exact[\"Complex\"] != df_exact[\"Complex_from_complex_clean\"])\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rows where Complex_from_complex exists but Complex is missing: 185\n" + ] + } + ], + "source": [ + "rows = df_exact[\n", + " df_exact[\"Complex\"].notna() &\n", + " df_exact[\"Complex_from_complex\"].isna()\n", + "]\n", + "\n", + "print(\"Rows where Complex_from_complex exists but Complex is missing:\", len(rows))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "df_exact populate the column Complex with Complex_from_complex_clean when Complex is empty or na and then drop cols seqA, seqB, k1, k2, Complex_from_complex_clean" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "# Populate in df_exact the column Complex with Complex_from_complex_clean when Complex is empty or na\n", + "\n", + "df_exact[\"Complex\"] = df_exact[\"Complex\"].replace(\"\", pd.NA)\n", + "df_exact[\"Complex_from_complex_clean\"] = df_exact[\"Complex_from_complex_clean\"].replace(\"\", pd.NA)\n", + "df_exact[\"Complex\"] = df_exact[\"Complex\"].combine_first(df_exact[\"Complex_from_complex_clean\"])\n", + "# # Drop helper columns\n", + "df_exact = df_exact.drop(columns=[\"seqA\", \"seqB\", \"k1\", \"k2\", 'Complex_from_complex', 'Interactor_chain_1','Interactor_1_seq',\t'Interactor_chain_2',\t'Interactor_2_seq'])\n", + "mask = df_exact[\"Complex_from_complex_clean\"].fillna(\"\") != df_exact[\"Complex\"].fillna(\"\")\n", + "\n", + "df_exact[\"Alternative_Complex\"] = None\n", + "df_exact.loc[mask, \"Alternative_Complex\"] = df_exact.loc[mask, \"Complex_from_complex_clean\"]\n", + "df_exact = df_exact.drop(columns=[\"Complex_from_complex_clean\"])" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "df_exact[\"hf_complex_path\"] = \"../data/ProteinStructures/Complexes/\" + df_exact[\"Complex\"].astype(str) + \".pdb\"\n" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "df = df_exact.copy()\n", + "\n", + "# 1) Read interface residues\n", + "iface = pd.read_csv(\n", + " \"../data/ProteinStructures/complex_interface.csv\"\n", + ")\n", + "\n", + "aa3_to_aa1 = {\n", + " \"ALA\":\"A\",\"ARG\":\"R\",\"ASN\":\"N\",\"ASP\":\"D\",\"CYS\":\"C\",\n", + " \"GLN\":\"Q\",\"GLU\":\"E\",\"GLY\":\"G\",\"HIS\":\"H\",\"ILE\":\"I\",\n", + " \"LEU\":\"L\",\"LYS\":\"K\",\"MET\":\"M\",\"PHE\":\"F\",\"PRO\":\"P\",\n", + " \"SER\":\"S\",\"THR\":\"T\",\"TRP\":\"W\",\"TYR\":\"Y\",\"VAL\":\"V\"\n", + "}\n", + "\n", + "iface[\"AA1\"] = iface[\"AA\"].map(aa3_to_aa1).fillna(\"X\")\n", + "\n", + "# ------------------------------------------------\n", + "# 2) interface_sites_num → {chain: \"site1,site2,...\"}\n", + "# ------------------------------------------------\n", + "\n", + "sites_agg = (\n", + " iface.groupby([\"Complex\", \"Chain\"])[\"Site\"]\n", + " .apply(lambda s: \",\".join(map(str, s.tolist())))\n", + " .reset_index(name=\"sites\")\n", + ")\n", + "\n", + "sites_dict = (\n", + " sites_agg.groupby(\"Complex\")\n", + " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"sites\"])))\n", + " .to_dict()\n", + ")\n", + "\n", + "df[\"interface_sites_num\"] = df[\"Complex\"].map(sites_dict).apply(\n", + " lambda x: x if isinstance(x, dict) else {}\n", + ")\n", + "\n", + "# ------------------------------------------------\n", + "# 3) interface_sequence_dict → {chain: \"A,S,T,...\"}\n", + "# ------------------------------------------------\n", + "\n", + "seq_agg = (\n", + " iface.groupby([\"Complex\", \"Chain\"])[\"AA1\"]\n", + " .apply(lambda s: \",\".join(s.tolist()))\n", + " .reset_index(name=\"seqs\")\n", + ")\n", + "\n", + "seq_dict = (\n", + " seq_agg.groupby(\"Complex\")\n", + " .apply(lambda g: dict(zip(g[\"Chain\"], g[\"seqs\"])))\n", + " .to_dict()\n", + ")\n", + "\n", + "df[\"interface_sequence_dict\"] = df[\"Complex\"].map(seq_dict).apply(\n", + " lambda x: x if isinstance(x, dict) else {}\n", + ")\n", + "\n", + "# normalize capitalization\n", + "df[\"Effect\"] = df[\"Effect\"].str.lower().str.capitalize()\n", + "# convert Induce -> Enhance\n", + "df[\"Effect\"] = df[\"Effect\"].replace(\"Induce\", \"Enhance\")" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rows with Complex: 4561\n", + "Rows without Complex: 595\n" + ] + } + ], + "source": [ + "complex_col = df_exact[\"Complex\"].replace(\"\", pd.NA)\n", + "\n", + "num_with_complex = complex_col.notna().sum()\n", + "num_without_complex = complex_col.isna().sum()\n", + "\n", + "print(\"Rows with Complex:\", num_with_complex)\n", + "print(\"Rows without Complex:\", num_without_complex)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### 5. Filling missing information on whether the phosphorylation site is in the interface" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Rows with Complex: 4561\n", + "Rows lacking Complex: 595\n", + "Rows where interface missing: 3015\n" + ] + } + ], + "source": [ + "has_complex = df[\"Complex\"].notna() & (df[\"Complex\"].astype(str).str.strip() != \"\")\n", + "print(\"Rows with Complex:\", has_complex.sum())\n", + "print(\"Rows lacking Complex:\", (~has_complex).sum())\n", + "\n", + "df_with_complex = df[has_complex].copy()\n", + "\n", + "interface_missing = (\n", + " df_with_complex[\"Interface\"].isna()\n", + " | df_with_complex[\"Interface\"].eq(\"\")\n", + ")\n", + "\n", + "print(\"Rows where interface missing:\", interface_missing.sum())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "pd.set_option('display.max_columns', None)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [], + "source": [ + "df_prev=df.copy()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffectMethodDiseaseCo-localizedPMIDCo_localizedComplexOriginConfidencePDBRESScoreInterfaceDomaininterface_sites_numinterface_sequence_dicthf_complex_pathGene_sequenceInt_gene_sequenceInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexAlternative_Complex
0HumanAANATQ16613Phos31TCQRRHtLPASEP63104YWHAZEnhanceMolecular dynamics simulation(MD)NaNNaN28387381NaNComplex2735PyMOLMediumA31:THR0.50TrueNaN{'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,...{'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E...../data/ProteinStructures/Complexes/Complex273...MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...AMSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...BMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...None
1HumanAATFQ9NY61Phos366TVYRNRtLQKWHP19105MYL12AInhibitPeptide pull-downEndometrial cancerNaN22909821NaNComplex3475ZDOCKLowA366:THR0.50FalseAATF-Che1{'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,...{'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D...../data/ProteinStructures/Complexes/Complex347...MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...AMAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...BMSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...None
2HumanABCG2Q9UNQ0Phos362TKKKKItVFKEIQ9UNQ0ABCG2EnhanceCo-IPProstate cancerPlasma membrane18056989Plasma membraneComplex3607PyMOLMediumA362:THR0.50FalseNaN{'A': '44,46,48,53,56,63,81,82,83,88,97,126,12...{'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q...../data/ProteinStructures/Complexes/Complex360...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...AMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...BMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...None
3HumanABI1Q8IZP0Phos213YTVPNDyMTSPAP27986PIK3R1EnhanceAffinity capture binding assayNaNNaN20598684NaNComplex2954ZDOCKLowB213:TYR0.50FalseNaN{'A': '1,363,364,365,620,621,622,625,626,627,6...{'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q...../data/ProteinStructures/Complexes/Complex295...MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...AMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...BMAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...None
4HumanABI3Q9P2A4Phos342SVTRRYsDGWCEQ7L576CYFIP1InhibitCo-IPThyroid cancerNaN28978070NaNComplex3517ZDOCKLowB342:SER0.75FalseSH3_9{'A': '781,782,785,788,831,832,833,834,835,836...{'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F...../data/ProteinStructures/Complexes/Complex351...MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...AMAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...BMAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...None
...................................................................................................
5151S. pombeKlp9Q1MTQ7Phos605SKKKVVsPIKPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...None
5152S. pombeKlp9Q1MTQ7Phos611SPIKPLsPSRRPQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...None
5153S. pombeKlp9Q1MTQ7Phos613SKPLSPsRRPPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...None
5154S. pombeCrb2P87074Phos73TEELSLtQLFEVP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...None
5155S. pombeCrb2P87074Phos80SLFEVPsQAAFAP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...None
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5156 rows × 32 columns

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" + ], + "text/plain": [ + " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", + "0 Human AANAT Q16613 Phos 31 T CQRRHtLPASE P63104 \n", + "1 Human AATF Q9NY61 Phos 366 T VYRNRtLQKWH P19105 \n", + "2 Human ABCG2 Q9UNQ0 Phos 362 T KKKKItVFKEI Q9UNQ0 \n", + "3 Human ABI1 Q8IZP0 Phos 213 Y TVPNDyMTSPA P27986 \n", + "4 Human ABI3 Q9P2A4 Phos 342 S VTRRYsDGWCE Q7L576 \n", + "... ... ... ... ... ... .. ... ... \n", + "5151 S. pombe Klp9 Q1MTQ7 Phos 605 S KKKVVsPIKPL Q9HDY1 \n", + "5152 S. pombe Klp9 Q1MTQ7 Phos 611 S PIKPLsPSRRP Q9HDY1 \n", + "5153 S. pombe Klp9 Q1MTQ7 Phos 613 S KPLSPsRRPPL Q9HDY1 \n", + "5154 S. pombe Crb2 P87074 Phos 73 T EELSLtQLFEV P34208 \n", + "5155 S. pombe Crb2 P87074 Phos 80 S LFEVPsQAAFA P34208 \n", + "\n", + " Int_gene Effect Method \\\n", + "0 YWHAZ Enhance Molecular dynamics simulation(MD) \n", + "1 MYL12A Inhibit Peptide pull-down \n", + "2 ABCG2 Enhance Co-IP \n", + "3 PIK3R1 Enhance Affinity capture binding assay \n", + "4 CYFIP1 Inhibit Co-IP \n", + "... ... ... ... \n", + "5151 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5152 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5153 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5154 Chk1 Enhance Peptide pull-down \n", + "5155 Chk1 Enhance Peptide pull-down \n", + "\n", + " Disease Co-localized PMID Co_localized \\\n", + "0 NaN NaN 28387381 NaN \n", + "1 Endometrial cancer NaN 22909821 NaN \n", + "2 Prostate cancer Plasma membrane 18056989 Plasma membrane \n", + "3 NaN NaN 20598684 NaN \n", + "4 Thyroid cancer NaN 28978070 NaN \n", + "... ... ... ... ... \n", + "5151 NaN Spindle midzone 19686686 NaN \n", + "5152 NaN Spindle midzone 19686686 NaN \n", + "5153 NaN Spindle midzone 19686686 NaN \n", + "5154 NaN NaN 22792081 NaN \n", + "5155 NaN NaN 22792081 NaN \n", + "\n", + " Complex Origin Confidence PDBRES Score Interface Domain \\\n", + "0 Complex2735 PyMOL Medium A31:THR 0.50 True NaN \n", + "1 Complex3475 ZDOCK Low A366:THR 0.50 False AATF-Che1 \n", + "2 Complex3607 PyMOL Medium A362:THR 0.50 False NaN \n", + "3 Complex2954 ZDOCK Low B213:TYR 0.50 False NaN \n", + "4 Complex3517 ZDOCK Low B342:SER 0.75 False SH3_9 \n", + "... ... ... ... ... ... ... ... \n", + "5151 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5152 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5153 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5154 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", + "5155 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", + "\n", + " interface_sites_num \\\n", + "0 {'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,... \n", + "1 {'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,... \n", + "2 {'A': '44,46,48,53,56,63,81,82,83,88,97,126,12... \n", + "3 {'A': '1,363,364,365,620,621,622,625,626,627,6... \n", + "4 {'A': '781,782,785,788,831,832,833,834,835,836... \n", + "... ... \n", + "5151 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5152 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5153 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5154 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", + "5155 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", + "\n", + " interface_sequence_dict \\\n", + "0 {'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E... \n", + "1 {'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D... \n", + "2 {'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q... \n", + "3 {'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q... \n", + "4 {'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F... \n", + "... ... \n", + "5151 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5152 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5153 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5154 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", + "5155 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", + "\n", + " hf_complex_path \\\n", + "0 ../data/ProteinStructures/Complexes/Complex273... \n", + "1 ../data/ProteinStructures/Complexes/Complex347... \n", + "2 ../data/ProteinStructures/Complexes/Complex360... \n", + "3 ../data/ProteinStructures/Complexes/Complex295... \n", + "4 ../data/ProteinStructures/Complexes/Complex351... \n", + "... ... \n", + "5151 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5152 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5153 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5154 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5155 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "\n", + " Gene_sequence \\\n", + "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", + "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... \n", + "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... \n", + "... ... \n", + "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "\n", + " Int_gene_sequence \\\n", + "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... \n", + "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", + "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", + "... ... \n", + "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", + "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", + "\n", + " Interactor_chain_1_from_complex \\\n", + "0 A \n", + "1 A \n", + "2 A \n", + "3 A \n", + "4 A \n", + "... ... \n", + "5151 A \n", + "5152 A \n", + "5153 A \n", + "5154 A \n", + "5155 A \n", + "\n", + " Interactor_1_seq_from_complex \\\n", + "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", + "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", + "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", + "... ... \n", + "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "\n", + " Interactor_chain_2_from_complex \\\n", + "0 B \n", + "1 B \n", + "2 B \n", + "3 B \n", + "4 B \n", + "... ... \n", + "5151 B \n", + "5152 B \n", + "5153 B \n", + "5154 B \n", + "5155 B \n", + "\n", + " Interactor_2_seq_from_complex Alternative_Complex \n", + "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... None \n", + "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... None \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... None \n", + "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... None \n", + "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... None \n", + "... ... ... \n", + "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", + "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", + "\n", + "[5156 rows x 32 columns]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import numpy as np\n", + "\n", + "def check_interface_site(row):\n", + "\n", + " site = int(row[\"Site\"])\n", + " aminoa = from AA\n", + " sites_dict = row[\"interface_sites_num\"]\n", + "\n", + " if pd.isna(sites_dict) or sites_dict == \"\" or sites_dict == {}:\n", + " return np.nan\n", + "\n", + " pdbres = row[\"PDBRES\"]\n", + "\n", + " # ---- case 1: PDBRES exists → use that chain ----\n", + " if isinstance(pdbres, str) and pdbres != \"\":\n", + " chain = pdbres[0] # first letter\n", + "\n", + " if chain not in sites_dict:\n", + " return \"False\"\n", + "\n", + " sites = sites_dict[chain]\n", + "\n", + " if isinstance(sites, str):\n", + " sites = [int(x) for x in sites.split(\",\")]\n", + "\n", + " if site in sites:\n", + " return \"True\"\n", + " else:\n", + " return \"False\"\n", + "\n", + " # ---- case 2: PDBRES missing → check all chains ----\n", + " else:\n", + "\n", + " for chain, sites in sites_dict.items():\n", + "\n", + " if isinstance(sites, str):\n", + " sites = [int(x) for x in sites.split(\",\")]\n", + "\n", + " if site in sites:\n", + " #check if amino acid aminoa is the same as the one from the site detected. can be obtained from dictionary from row[\"interface_sequence_dict\"]\n", + " return \"Possibly\"\n", + "\n", + " return \"False\"\n", + "\n", + "df[\"site_in_interface\"] = df.apply(check_interface_site, axis=1)" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffectMethodDiseaseCo-localizedPMIDCo_localizedComplexOriginConfidencePDBRESScoreInterfaceDomaininterface_sites_numinterface_sequence_dicthf_complex_pathGene_sequenceInt_gene_sequenceInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexAlternative_Complexsite_in_interface
0HumanAANATQ16613Phos31TCQRRHtLPASEP63104YWHAZEnhanceMolecular dynamics simulation(MD)NaNNaN28387381NaNComplex2735PyMOLMediumA31:THR0.50TrueNaN{'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,...{'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E...../data/ProteinStructures/Complexes/Complex273...MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...AMSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...BMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...NoneTrue
1HumanAATFQ9NY61Phos366TVYRNRtLQKWHP19105MYL12AInhibitPeptide pull-downEndometrial cancerNaN22909821NaNComplex3475ZDOCKLowA366:THR0.50FalseAATF-Che1{'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,...{'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D...../data/ProteinStructures/Complexes/Complex347...MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...AMAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...BMSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...NoneFalse
2HumanABCG2Q9UNQ0Phos362TKKKKItVFKEIQ9UNQ0ABCG2EnhanceCo-IPProstate cancerPlasma membrane18056989Plasma membraneComplex3607PyMOLMediumA362:THR0.50FalseNaN{'A': '44,46,48,53,56,63,81,82,83,88,97,126,12...{'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q...../data/ProteinStructures/Complexes/Complex360...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...AMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...BMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...NoneFalse
3HumanABI1Q8IZP0Phos213YTVPNDyMTSPAP27986PIK3R1EnhanceAffinity capture binding assayNaNNaN20598684NaNComplex2954ZDOCKLowB213:TYR0.50FalseNaN{'A': '1,363,364,365,620,621,622,625,626,627,6...{'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q...../data/ProteinStructures/Complexes/Complex295...MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...AMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...BMAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...NoneFalse
4HumanABI3Q9P2A4Phos342SVTRRYsDGWCEQ7L576CYFIP1InhibitCo-IPThyroid cancerNaN28978070NaNComplex3517ZDOCKLowB342:SER0.75FalseSH3_9{'A': '781,782,785,788,831,832,833,834,835,836...{'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F...../data/ProteinStructures/Complexes/Complex351...MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...AMAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...BMAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...NoneFalse
......................................................................................................
5151S. pombeKlp9Q1MTQ7Phos605SKKKVVsPIKPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5152S. pombeKlp9Q1MTQ7Phos611SPIKPLsPSRRPQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5153S. pombeKlp9Q1MTQ7Phos613SKPLSPsRRPPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5154S. pombeCrb2P87074Phos73TEELSLtQLFEVP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
5155S. pombeCrb2P87074Phos80SLFEVPsQAAFAP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
\n", + "

5156 rows × 33 columns

\n", + "
" + ], + "text/plain": [ + " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", + "0 Human AANAT Q16613 Phos 31 T CQRRHtLPASE P63104 \n", + "1 Human AATF Q9NY61 Phos 366 T VYRNRtLQKWH P19105 \n", + "2 Human ABCG2 Q9UNQ0 Phos 362 T KKKKItVFKEI Q9UNQ0 \n", + "3 Human ABI1 Q8IZP0 Phos 213 Y TVPNDyMTSPA P27986 \n", + "4 Human ABI3 Q9P2A4 Phos 342 S VTRRYsDGWCE Q7L576 \n", + "... ... ... ... ... ... .. ... ... \n", + "5151 S. pombe Klp9 Q1MTQ7 Phos 605 S KKKVVsPIKPL Q9HDY1 \n", + "5152 S. pombe Klp9 Q1MTQ7 Phos 611 S PIKPLsPSRRP Q9HDY1 \n", + "5153 S. pombe Klp9 Q1MTQ7 Phos 613 S KPLSPsRRPPL Q9HDY1 \n", + "5154 S. pombe Crb2 P87074 Phos 73 T EELSLtQLFEV P34208 \n", + "5155 S. pombe Crb2 P87074 Phos 80 S LFEVPsQAAFA P34208 \n", + "\n", + " Int_gene Effect Method \\\n", + "0 YWHAZ Enhance Molecular dynamics simulation(MD) \n", + "1 MYL12A Inhibit Peptide pull-down \n", + "2 ABCG2 Enhance Co-IP \n", + "3 PIK3R1 Enhance Affinity capture binding assay \n", + "4 CYFIP1 Inhibit Co-IP \n", + "... ... ... ... \n", + "5151 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5152 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5153 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5154 Chk1 Enhance Peptide pull-down \n", + "5155 Chk1 Enhance Peptide pull-down \n", + "\n", + " Disease Co-localized PMID Co_localized \\\n", + "0 NaN NaN 28387381 NaN \n", + "1 Endometrial cancer NaN 22909821 NaN \n", + "2 Prostate cancer Plasma membrane 18056989 Plasma membrane \n", + "3 NaN NaN 20598684 NaN \n", + "4 Thyroid cancer NaN 28978070 NaN \n", + "... ... ... ... ... \n", + "5151 NaN Spindle midzone 19686686 NaN \n", + "5152 NaN Spindle midzone 19686686 NaN \n", + "5153 NaN Spindle midzone 19686686 NaN \n", + "5154 NaN NaN 22792081 NaN \n", + "5155 NaN NaN 22792081 NaN \n", + "\n", + " Complex Origin Confidence PDBRES Score Interface Domain \\\n", + "0 Complex2735 PyMOL Medium A31:THR 0.50 True NaN \n", + "1 Complex3475 ZDOCK Low A366:THR 0.50 False AATF-Che1 \n", + "2 Complex3607 PyMOL Medium A362:THR 0.50 False NaN \n", + "3 Complex2954 ZDOCK Low B213:TYR 0.50 False NaN \n", + "4 Complex3517 ZDOCK Low B342:SER 0.75 False SH3_9 \n", + "... ... ... ... ... ... ... ... \n", + "5151 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5152 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5153 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5154 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", + "5155 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", + "\n", + " interface_sites_num \\\n", + "0 {'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,... \n", + "1 {'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,... \n", + "2 {'A': '44,46,48,53,56,63,81,82,83,88,97,126,12... \n", + "3 {'A': '1,363,364,365,620,621,622,625,626,627,6... \n", + "4 {'A': '781,782,785,788,831,832,833,834,835,836... \n", + "... ... \n", + "5151 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5152 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5153 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5154 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", + "5155 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", + "\n", + " interface_sequence_dict \\\n", + "0 {'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E... \n", + "1 {'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D... \n", + "2 {'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q... \n", + "3 {'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q... \n", + "4 {'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F... \n", + "... ... \n", + "5151 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5152 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5153 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5154 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", + "5155 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", + "\n", + " hf_complex_path \\\n", + "0 ../data/ProteinStructures/Complexes/Complex273... \n", + "1 ../data/ProteinStructures/Complexes/Complex347... \n", + "2 ../data/ProteinStructures/Complexes/Complex360... \n", + "3 ../data/ProteinStructures/Complexes/Complex295... \n", + "4 ../data/ProteinStructures/Complexes/Complex351... \n", + "... ... \n", + "5151 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5152 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5153 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5154 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5155 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "\n", + " Gene_sequence \\\n", + "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", + "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... \n", + "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... \n", + "... ... \n", + "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "\n", + " Int_gene_sequence \\\n", + "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... \n", + "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", + "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", + "... ... \n", + "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", + "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", + "\n", + " Interactor_chain_1_from_complex \\\n", + "0 A \n", + "1 A \n", + "2 A \n", + "3 A \n", + "4 A \n", + "... ... \n", + "5151 A \n", + "5152 A \n", + "5153 A \n", + "5154 A \n", + "5155 A \n", + "\n", + " Interactor_1_seq_from_complex \\\n", + "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", + "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", + "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", + "... ... \n", + "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "\n", + " Interactor_chain_2_from_complex \\\n", + "0 B \n", + "1 B \n", + "2 B \n", + "3 B \n", + "4 B \n", + "... ... \n", + "5151 B \n", + "5152 B \n", + "5153 B \n", + "5154 B \n", + "5155 B \n", + "\n", + " Interactor_2_seq_from_complex Alternative_Complex \\\n", + "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... None \n", + "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... None \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... None \n", + "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... None \n", + "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... None \n", + "... ... ... \n", + "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", + "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", + "\n", + " site_in_interface \n", + "0 True \n", + "1 False \n", + "2 False \n", + "3 False \n", + "4 False \n", + "... ... \n", + "5151 False \n", + "5152 False \n", + "5153 False \n", + "5154 False \n", + "5155 False \n", + "\n", + "[5156 rows x 33 columns]" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[1468, 1469, 1470, 1473, 1474, 1476, 1477, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510, 1511, 1512, 1513, 1514, 1516, 1517, 1518, 1519, 1521, 1522, 1525, 1527, 1528, 1529]\n", + "APC ['K', 'Q', 'A', 'N', 'A', 'V', 'Q', 'Q', 'V', 'L', 'P', 'D', 'A', 'D', 'X', 'L', 'L', 'H', 'F', 'A', 'T', 'E', 'S', 'T', 'S', 'X', 'X', 'L', 'X', 'A', 'L', 'X', 'L', 'D', 'E', 'P', 'I', 'Q', 'K', 'D', 'E', 'L', 'M', 'P', 'V', 'Q']\n", + "Mismatch | Gene=APC | Site=1505 | Expected=S | Found=X\n", + "[1468, 1469, 1470, 1473, 1474, 1476, 1477, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510, 1511, 1512, 1513, 1514, 1516, 1517, 1518, 1519, 1521, 1522, 1525, 1527, 1528, 1529]\n", + "APC ['K', 'Q', 'A', 'N', 'A', 'V', 'Q', 'Q', 'V', 'L', 'P', 'D', 'A', 'D', 'X', 'L', 'L', 'H', 'F', 'A', 'T', 'E', 'S', 'T', 'S', 'X', 'X', 'L', 'X', 'A', 'L', 'X', 'L', 'D', 'E', 'P', 'I', 'Q', 'K', 'D', 'E', 'L', 'M', 'P', 'V', 'Q']\n", + "Mismatch | Gene=APC | Site=1507 | Expected=S | Found=X\n", + "[764, 765, 767, 768, 769, 770, 772]\n", + "CFTR ['R', 'R', 'Q', 'X', 'V', 'L', 'L']\n", + "Mismatch | Gene=CFTR | Site=768 | Expected=S | Found=X\n", + "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", + "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", + "Mismatch | Gene=ERRFI1 | Site=394 | Expected=Y | Found=X\n", + "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", + "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", + "Mismatch | Gene=ERRFI1 | Site=394 | Expected=Y | Found=X\n", + "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", + "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", + "Mismatch | Gene=ERRFI1 | Site=395 | Expected=Y | Found=X\n", + "[336, 337, 338, 339, 341, 344, 346, 347, 348, 349, 350, 351, 352, 353, 356, 357, 358, 359, 360, 376, 377, 379, 382, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398]\n", + "ERRFI1 ['K', 'S', 'L', 'P', 'Y', 'G', 'M', 'P', 'P', 'T', 'Q', 'S', 'F', 'A', 'P', 'K', 'Y', 'V', 'S', 'V', 'P', 'I', 'I', 'V', 'C', 'S', 'T', 'H', 'X', 'X', 'L', 'L', 'P']\n", + "Mismatch | Gene=ERRFI1 | Site=395 | Expected=Y | Found=X\n", + "[695, 699, 702, 703, 704, 706, 707, 709, 710, 711, 712, 725, 727, 728, 730, 731, 732, 733, 734, 1045, 1046, 1049, 1052, 1053, 1056, 1061, 1062, 1063, 1064, 1065, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1106, 1107, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1383, 1385, 1386, 1387, 1388, 1389, 1390, 1391]\n", + "ESPL1 ['E', 'R', 'R', 'A', 'Q', 'P', 'G', 'L', 'E', 'E', 'F', 'E', 'R', 'F', 'Y', 'S', 'N', 'I', 'A', 'D', 'L', 'S', 'Q', 'Q', 'F', 'C', 'T', 'E', 'F', 'G', 'E', 'L', 'F', 'L', 'R', 'G', 'P', 'L', 'E', 'V', 'A', 'T', 'V', 'A', 'K', 'E', 'P', 'G', 'P', 'I', 'P', 'S', 'S', 'X', 'P', 'V', 'L', 'K', 'T', 'K', 'V', 'Q', 'R', 'V', 'Q', 'T', 'R', 'L']\n", + "Mismatch | Gene=ESPL1 | Site=1126 | Expected=S | Found=X\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "import numpy as np\n", + "\n", + "def check_interface_site(row):\n", + "\n", + " site = int(row[\"Site\"])\n", + " aminoa = row[\"AA\"]\n", + " sites_dict = row[\"interface_sites_num\"]\n", + " seq_dict = row[\"interface_sequence_dict\"]\n", + "\n", + " if pd.isna(sites_dict) or sites_dict == \"\" or sites_dict == {}:\n", + " return np.nan\n", + "\n", + " pdbres = row[\"PDBRES\"]\n", + "\n", + " # ---- case 1: PDBRES exists → use that chain ----\n", + " if isinstance(pdbres, str) and pdbres != \"\":\n", + " chain = pdbres[0] # first letter\n", + "\n", + " if chain not in sites_dict:\n", + " return \"False\"\n", + "\n", + " sites = sites_dict[chain]\n", + " seq = seq_dict[chain]\n", + " if isinstance(sites, str):\n", + " sites = [int(x) for x in sites.split(\",\")]\n", + "\n", + " if isinstance(seq, str):\n", + " seq = [str(x) for x in seq.split(\",\")]\n", + "\n", + " if site in sites:\n", + " idx = sites.index(site)\n", + " aa_interface = seq[idx]\n", + "\n", + " if aa_interface.upper() == aminoa.upper():\n", + " return \"True\"\n", + " else:\n", + " print(sites)\n", + " print(row['Gene'], seq)\n", + " print(f\"Mismatch | Gene={row['Gene']} | Site={site} | Expected={aminoa} | Found={aa_interface}\")\n", + " return \"False\"\n", + " else:\n", + " return \"False\"\n", + "\n", + " # ---- case 2: PDBRES missing → check all chains ----\n", + " else:\n", + " found = False\n", + " for chain, sites in sites_dict.items():\n", + " if isinstance(sites, str):\n", + " sites = [int(x) for x in sites.split(\",\")]\n", + "\n", + " if site in sites:\n", + " seq = seq_dict[chain]\n", + "\n", + " if isinstance(seq, str):\n", + " seq = [str(x) for x in seq.split(\",\")]\n", + "\n", + " idx = sites.index(site)\n", + " aa_interface = seq[idx]\n", + "\n", + " if aa_interface.upper() == aminoa.upper():\n", + " found = True\n", + " return \"True\"\n", + " if found:\n", + " print(f\"Gene={row['Gene']} | Site={site} | Expected={aminoa} | Found={aa_interface} | COMPLEX={row['Complex']}\")\n", + " print(f'found in chain {chain}')\n", + " return \"False\"\n", + "\n", + "df[\"site_in_interface\"] = df.apply(check_interface_site, axis=1)" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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OrganismGeneUniprotPTMSiteAASequenceWindowInt_uniprotInt_geneEffectMethodDiseaseCo-localizedPMIDCo_localizedComplexOriginConfidencePDBRESScoreInterfaceDomaininterface_sites_numinterface_sequence_dicthf_complex_pathGene_sequenceInt_gene_sequenceInteractor_chain_1_from_complexInteractor_1_seq_from_complexInteractor_chain_2_from_complexInteractor_2_seq_from_complexAlternative_Complexsite_in_interface
0HumanAANATQ16613Phos31TCQRRHtLPASEP63104YWHAZEnhanceMolecular dynamics simulation(MD)NaNNaN28387381NaNComplex2735PyMOLMediumA31:THR0.50TrueNaN{'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,...{'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E...../data/ProteinStructures/Complexes/Complex273...MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...AMSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV...BMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV...NoneTrue
1HumanAATFQ9NY61Phos366TVYRNRtLQKWHP19105MYL12AInhibitPeptide pull-downEndometrial cancerNaN22909821NaNComplex3475ZDOCKLowA366:THR0.50FalseAATF-Che1{'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,...{'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D...../data/ProteinStructures/Complexes/Complex347...MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...AMAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG...BMSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG...NoneFalse
2HumanABCG2Q9UNQ0Phos362TKKKKItVFKEIQ9UNQ0ABCG2EnhanceCo-IPProstate cancerPlasma membrane18056989Plasma membraneComplex3607PyMOLMediumA362:THR0.50FalseNaN{'A': '44,46,48,53,56,63,81,82,83,88,97,126,12...{'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q...../data/ProteinStructures/Complexes/Complex360...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...AMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...BMSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV...NoneFalse
3HumanABI1Q8IZP0Phos213YTVPNDyMTSPAP27986PIK3R1EnhanceAffinity capture binding assayNaNNaN20598684NaNComplex2954ZDOCKLowB213:TYR0.50FalseNaN{'A': '1,363,364,365,620,621,622,625,626,627,6...{'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q...../data/ProteinStructures/Complexes/Complex295...MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...AMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ...BMAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA...NoneFalse
4HumanABI3Q9P2A4Phos342SVTRRYsDGWCEQ7L576CYFIP1InhibitCo-IPThyroid cancerNaN28978070NaNComplex3517ZDOCKLowB342:SER0.75FalseSH3_9{'A': '781,782,785,788,831,832,833,834,835,836...{'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F...../data/ProteinStructures/Complexes/Complex351...MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...AMAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF...BMAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA...NoneFalse
......................................................................................................
5151S. pombeKlp9Q1MTQ7Phos605SKKKVVsPIKPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5152S. pombeKlp9Q1MTQ7Phos611SPIKPLsPSRRPQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5153S. pombeKlp9Q1MTQ7Phos613SKPLSPsRRPPLQ9HDY1Ase1InhibitGST pull-down, Flourescence recovery after pho...NaNSpindle midzone19686686NaNSP_Complex1NaNNaNNaNNaNNaNNaN{'A': '336,339,340,342,343,345,362,363,365,366...{'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L...../data/ProteinStructures/Complexes/SP_Complex...MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...AMQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER...BMIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS...NoneFalse
5154S. pombeCrb2P87074Phos73TEELSLtQLFEVP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
5155S. pombeCrb2P87074Phos80SLFEVPsQAAFAP34208Chk1EnhancePeptide pull-downNaNNaN22792081NaNSP_Complex4NaNNaNNaNNaNNaNNaN{'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,...{'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L...../data/ProteinStructures/Complexes/SP_Complex...MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...AMEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR...BMAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT...NoneFalse
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5156 rows × 33 columns

\n", + "
" + ], + "text/plain": [ + " Organism Gene Uniprot PTM Site AA SequenceWindow Int_uniprot \\\n", + "0 Human AANAT Q16613 Phos 31 T CQRRHtLPASE P63104 \n", + "1 Human AATF Q9NY61 Phos 366 T VYRNRtLQKWH P19105 \n", + "2 Human ABCG2 Q9UNQ0 Phos 362 T KKKKItVFKEI Q9UNQ0 \n", + "3 Human ABI1 Q8IZP0 Phos 213 Y TVPNDyMTSPA P27986 \n", + "4 Human ABI3 Q9P2A4 Phos 342 S VTRRYsDGWCE Q7L576 \n", + "... ... ... ... ... ... .. ... ... \n", + "5151 S. pombe Klp9 Q1MTQ7 Phos 605 S KKKVVsPIKPL Q9HDY1 \n", + "5152 S. pombe Klp9 Q1MTQ7 Phos 611 S PIKPLsPSRRP Q9HDY1 \n", + "5153 S. pombe Klp9 Q1MTQ7 Phos 613 S KPLSPsRRPPL Q9HDY1 \n", + "5154 S. pombe Crb2 P87074 Phos 73 T EELSLtQLFEV P34208 \n", + "5155 S. pombe Crb2 P87074 Phos 80 S LFEVPsQAAFA P34208 \n", + "\n", + " Int_gene Effect Method \\\n", + "0 YWHAZ Enhance Molecular dynamics simulation(MD) \n", + "1 MYL12A Inhibit Peptide pull-down \n", + "2 ABCG2 Enhance Co-IP \n", + "3 PIK3R1 Enhance Affinity capture binding assay \n", + "4 CYFIP1 Inhibit Co-IP \n", + "... ... ... ... \n", + "5151 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5152 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5153 Ase1 Inhibit GST pull-down, Flourescence recovery after pho... \n", + "5154 Chk1 Enhance Peptide pull-down \n", + "5155 Chk1 Enhance Peptide pull-down \n", + "\n", + " Disease Co-localized PMID Co_localized \\\n", + "0 NaN NaN 28387381 NaN \n", + "1 Endometrial cancer NaN 22909821 NaN \n", + "2 Prostate cancer Plasma membrane 18056989 Plasma membrane \n", + "3 NaN NaN 20598684 NaN \n", + "4 Thyroid cancer NaN 28978070 NaN \n", + "... ... ... ... ... \n", + "5151 NaN Spindle midzone 19686686 NaN \n", + "5152 NaN Spindle midzone 19686686 NaN \n", + "5153 NaN Spindle midzone 19686686 NaN \n", + "5154 NaN NaN 22792081 NaN \n", + "5155 NaN NaN 22792081 NaN \n", + "\n", + " Complex Origin Confidence PDBRES Score Interface Domain \\\n", + "0 Complex2735 PyMOL Medium A31:THR 0.50 True NaN \n", + "1 Complex3475 ZDOCK Low A366:THR 0.50 False AATF-Che1 \n", + "2 Complex3607 PyMOL Medium A362:THR 0.50 False NaN \n", + "3 Complex2954 ZDOCK Low B213:TYR 0.50 False NaN \n", + "4 Complex3517 ZDOCK Low B342:SER 0.75 False SH3_9 \n", + "... ... ... ... ... ... ... ... \n", + "5151 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5152 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5153 SP_Complex1 NaN NaN NaN NaN NaN NaN \n", + "5154 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", + "5155 SP_Complex4 NaN NaN NaN NaN NaN NaN \n", + "\n", + " interface_sites_num \\\n", + "0 {'A': '16,22,25,27,28,29,30,31,32,33,34,35,36,... \n", + "1 {'A': '65,69,70,71,72,73,74,75,76,78,81,82,84,... \n", + "2 {'A': '44,46,48,53,56,63,81,82,83,88,97,126,12... \n", + "3 {'A': '1,363,364,365,620,621,622,625,626,627,6... \n", + "4 {'A': '781,782,785,788,831,832,833,834,835,836... \n", + "... ... \n", + "5151 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5152 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5153 {'A': '336,339,340,342,343,345,362,363,365,366... \n", + "5154 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", + "5155 {'A': '22,23,24,25,26,27,28,29,31,32,33,34,35,... \n", + "\n", + " interface_sequence_dict \\\n", + "0 {'A': 'L,E,S,Q,R,R,H,T,L,P,A,S,E,R,P,E,D,V,S,E... \n", + "1 {'A': 'L,K,R,Y,C,G,K,T,T,R,W,N,D,H,W,E,Q,T,L,D... \n", + "2 {'A': 'Y,V,L,L,R,I,P,T,G,S,K,Q,D,R,Q,E,G,D,K,Q... \n", + "3 {'A': 'M,K,M,H,D,E,K,N,V,G,S,S,N,R,N,K,E,L,E,Q... \n", + "4 {'A': 'E,L,G,E,N,V,S,A,P,Y,R,T,L,H,F,W,N,Y,P,F... \n", + "... ... \n", + "5151 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5152 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5153 {'A': 'Y,E,Q,K,S,T,N,Y,K,Q,A,E,S,A,K,S,S,L,R,L... \n", + "5154 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", + "5155 {'A': 'F,G,A,Q,A,A,I,S,N,N,Y,S,K,V,N,A,S,I,N,L... \n", + "\n", + " hf_complex_path \\\n", + "0 ../data/ProteinStructures/Complexes/Complex273... \n", + "1 ../data/ProteinStructures/Complexes/Complex347... \n", + "2 ../data/ProteinStructures/Complexes/Complex360... \n", + "3 ../data/ProteinStructures/Complexes/Complex295... \n", + "4 ../data/ProteinStructures/Complexes/Complex351... \n", + "... ... \n", + "5151 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5152 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5153 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5154 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "5155 ../data/ProteinStructures/Complexes/SP_Complex... \n", + "\n", + " Gene_sequence \\\n", + "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", + "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... \n", + "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... \n", + "... ... \n", + "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... \n", + "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "\n", + " Int_gene_sequence \\\n", + "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... \n", + "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", + "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", + "... ... \n", + "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", + "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... \n", + "\n", + " Interactor_chain_1_from_complex \\\n", + "0 A \n", + "1 A \n", + "2 A \n", + "3 A \n", + "4 A \n", + "... ... \n", + "5151 A \n", + "5152 A \n", + "5153 A \n", + "5154 A \n", + "5155 A \n", + "\n", + " Interactor_1_seq_from_complex \\\n", + "0 MSTQSTHPLKPEAPRLPPGIPESPSCQRRHTLPASEFRCLTPEDAV... \n", + "1 MAGPQPLALQLEQLLNPRPSEADPEADPEEATAARVIDRFDEGEDG... \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... \n", + "3 MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQ... \n", + "4 MAAQVTLEDALSNVDLLEELPLPDQQPCIEPPPSSLLYQPNFNTNF... \n", + "... ... \n", + "5151 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5152 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5153 MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIER... \n", + "5154 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "5155 MEVNDTSLHKGFGLDINSQRVFGAQAAISRNNYSKVNASINPSPPR... \n", + "\n", + " Interactor_chain_2_from_complex \\\n", + "0 B \n", + "1 B \n", + "2 B \n", + "3 B \n", + "4 B \n", + "... ... \n", + "5151 B \n", + "5152 B \n", + "5153 B \n", + "5154 B \n", + "5155 B \n", + "\n", + " Interactor_2_seq_from_complex Alternative_Complex \\\n", + "0 MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSV... None \n", + "1 MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDG... None \n", + "2 MSSSNVEVFIPVSQGNTNGFPATASNDLKAFTEGAVLSFHNICYRV... None \n", + "3 MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKA... None \n", + "4 MAELQQLQEFEIPTGREALRGNHSALLRVADYCEDNYVQATDKRKA... None \n", + "... ... ... \n", + "5151 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5152 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5153 MIQIFLRVKKAQPSSDASNKYGFLTVLNDYEILLESPEDSHAYRVS... None \n", + "5154 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", + "5155 MAQKLDNFPYHIGREIGTGAFASVRLCYDDNAKIYAVKFVNKKHAT... None \n", + "\n", + " site_in_interface \n", + "0 True \n", + "1 False \n", + "2 False \n", + "3 False \n", + "4 False \n", + "... ... \n", + "5151 False \n", + "5152 False \n", + "5153 False \n", + "5154 False \n", + "5155 False \n", + "\n", + "[5156 rows x 33 columns]" + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pd.set_option('display.max_colwidth', None)\n", + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [], + "source": [ + "df.to_csv(\"../data/ptmint_final.csv\", index=False)" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import matplotlib.pyplot as plt\n", + "\n", + "counts = df[\"site_in_interface\"].value_counts(dropna=False)\n", + "\n", + "counts.plot(kind=\"bar\")\n", + "\n", + "plt.xlabel(\"Site in Interface\")\n", + "plt.ylabel(\"Count\")\n", + "plt.title(\"Distribution of PTM Sites in Interface\")\n", + "plt.xticks(rotation=0)\n", + "\n", + "plt.show()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.18" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +}