SNFG stringlengths 26 26 | torsion_table stringlengths 39 39 | torsion_analysis stringlengths 2 10.3k | glytoucan stringlengths 8 8 ⌀ | ID stringlengths 7 7 | name stringlengths 10 243 | glycam stringlengths 5 238 | iupac stringlengths 3 236 | iupac_extended stringlengths 5 364 ⌀ | wurcs stringlengths 26 311 ⌀ | glycoct stringlengths 21 1.07k ⌀ | smiles stringlengths 30 1.05k ⌀ | oxford nullclasses 53
values | mass float64 150 4.19k ⌀ | motifs stringclasses 112
values | termini stringlengths 9 68 ⌀ | components stringlengths 10 100 | composition stringlengths 2 60 ⌀ | rot_bonds float64 0 73 ⌀ | hbond_donor float64 3 63 ⌀ | hbond_acceptor float64 5 102 ⌀ | entropy float64 4.68 15.6 | clusters stringlengths 2 100 | coverage_clusters stringlengths 2 929 | silhouette_scores stringlengths 171 182 | coverage_clusters_per_main stringlengths 52 197 | pca_variance stringlengths 478 497 | length float64 0 8 | package stringclasses 2
values | forcefield stringclasses 3
values | temperature float64 300 300 ⌀ | pressure float64 1 1 ⌀ | salt stringclasses 5
values | a_glycam stringlengths 10 243 | a_iupac stringlengths 7 240 | a_iupac_extended stringlengths 12 349 ⌀ | a_glytoucan stringlengths 8 8 ⌀ | a_wurcs stringlengths 33 318 ⌀ | b_glycam stringlengths 10 243 | b_iupac stringlengths 7 240 | b_iupac_extended stringlengths 12 371 ⌀ | b_glytoucan stringlengths 8 8 ⌀ | b_wurcs stringlengths 33 293 ⌀ | common_names nullclasses 66
values | description null | keywords stringclasses 11
values | calculated_torsion stringlengths 2 15.5k | a_calculated_torsion stringlengths 2 14.2k | b_calculated_torsion stringlengths 2 14.2k | glycosmos stringlengths 141 4.9k ⌀ | number_monosaccharides float64 1 21 ⌀ | species stringlengths 269 4.28k ⌀ | classification stringclasses 53
values | enzyme stringlengths 1.64k 35.6k ⌀ | crossref stringlengths 322 13.7k ⌀ | mass_pme float64 206 5.1k ⌀ | tool_support stringclasses 12
values | missing_score float64 93 1.97k ⌀ | glycan_type stringclasses 2
values | byonic stringlengths 20 54 ⌀ | gwb stringlengths 36 314 ⌀ | motifs.1 stringclasses 102
values | subsumption stringlengths 383 2.39k ⌀ | section_stats stringclasses 8
values | history stringclasses 9
values |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
./raw_dataGS00001/snfg.svg | ./torsion_data/GS00001_torsion_data.txt | {'Cluster 0': {'count': 14279, '3_2_phi_mean': -73.78, '3_2_psi_mean': 118.16, '3_2_phi_std': 13.23, '3_2_psi_std': 16.53}, 'Cluster 1': {'count': 10687, '3_2_phi_mean': -75.82, '3_2_psi_mean': 116.95, '3_2_phi_std': 17.6, '3_2_psi_std': 17.15}, 'Cluster 2': {'count': 8711, '3_2_phi_mean': -78.63, '3_2_psi_mean': 121.8... | G38695WE | GS00001 | DNeup5Gca2-3DGalpb1-4DGlcpa1-OH | DNeup5Gca2-3DGalpb1-4DGlcp | Neu5Gc(a2-3)Gal(b1-4)Glc | α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-D-Glc | WURCS=2.0/3,3,2/[u2122h][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a4-b1_b3-c2 | RES,1b:b-dglc-HEX-1:5,2b:b-dgal-HEX-1:5,3b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,4s:n-glycolyl,LIN,1:1o(4+1)2d,2:2o(3+2)3d,3:3d(5+1)4n, | O1C(O)[C@H](O)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(=O)CO)[C@H]([C@H](O)[C@H](O)CO)O3)[C@H]2O)[C@H]1CO | null | 649.21 | null | Neu5Gc(a2-3) | {'Neu5Gc': 1, 'Gal': 1, 'Glc': 1} | {'Hex': 2, 'Neu5Gc': 1} | 12 | 14 | 20 | 10.065379 | {'Cluster 0': 35.69, 'Cluster 1': 26.71, 'Cluster 2': 21.78, 'Cluster 3': 12.18, 'Cluster 4': 3.63} | {'Cluster 0': 36.7488, 'Cluster 1': 21.6478, 'Cluster 2': 18.4257, 'Cluster 3': 8.4517, 'Cluster 4': 5.9144, 'Cluster 5': 3.7871, 'Cluster 6': 1.5498, 'Cluster 7': 1.1749, 'Cluster 8': 0.8124, 'Cluster 9': 0.6424, 'Cluster 10': 0.5549, 'Cluster 11': 0.145, 'Cluster 12': 0.1125, 'Cluster 13': 0.0325} | {'2': 0.3743617290500686, '3': 0.45777173998767523, '4': 0.4726679052710324, '5': 0.3790089243138171, '6': 0.35333630072941075, '7': 0.3519328541390717, '8': 0.3008343406916214} | {'0': [0, 8], '1': [4, 5, 13], '2': [2, 6, 9, 10], '3': [], '4': [1, 3, 7, 11, 12]} | {'explained_variance_ratio': [0.18115023375391787, 0.13429807144402506, 0.05944877857088233, 0.0458009543984269, 0.04396628214163917, 0.039212355211333316, 0.028738340455322968, 0.027442605146435633, 0.023284288855357136, 0.019321717847951395], 'cumulative_variance': [0.18115023375391787, 0.3154483051979429, 0.37489708... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | 150 | DNeup5Gca2-3DGalpb1-4DGlcpa1-OH | Neu5Gc(a2-3)Gal(b1-4)Glc(a1- | α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-α-D-Glcp-(1→ | G50281RU | WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a4-b1_b3-c2 | DNeup5Gca2-3DGalpb1-4DGlcpb1-OH | Neu5Gc(a2-3)Gal(b1-4)Glc(b1- | α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ | G75789AR | WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a4-b1_b3-c2 | null | null | null | {'GLC2-GAL3': {'2': {'phi': -68.91, 'psi': 129.96, 'strain': 0.031, 'linkage': '1-4'}, '3': {'phi': -75.01, 'psi': 119.06, 'strain': -0.0, 'linkage': '1-4'}, '4': {'phi': -76.98, 'psi': 146.96, 'strain': 1.078, 'linkage': '1-4'}, '5': {'phi': -64.73, 'psi': 125.13, 'strain': 0.031, 'linkage': '1-4'}, '6': {'phi': -55.7... | {'GLC2-GAL3': {'2': {'phi': -68.91, 'psi': 129.96, 'strain': 0.031, 'linkage': '1-4'}, '3': {'phi': -74.97, 'psi': 119.07, 'strain': -0.0, 'linkage': '1-4'}, '4': {'phi': -76.95, 'psi': 146.88, 'strain': 1.078, 'linkage': '1-4'}, '5': {'phi': -64.76, 'psi': 125.18, 'strain': 0.031, 'linkage': '1-4'}, '6': {'phi': -55.7... | {'GLC2-GAL3': {'2': {'phi': -68.91, 'psi': 129.96, 'strain': 0.031, 'linkage': '1-4'}, '3': {'phi': -75.01, 'psi': 119.06, 'strain': -0.0, 'linkage': '1-4'}, '4': {'phi': -76.98, 'psi': 146.96, 'strain': 1.078, 'linkage': '1-4'}, '5': {'phi': -64.73, 'psi': 125.13, 'strain': 0.031, 'linkage': '1-4'}, '6': {'phi': -55.7... | {'taxon_id': '10114', 'taxon_label': 'Rattus', 'evidence': [{'label': 'GlyTouCan(glycome-db)', 'id': 'glytoucan.org/Structures/Glycans/G38695WE'}]};{'taxon_id': '562', 'taxon_label': 'Escherichia coli', 'evidence': [{'label': 'GlyTouCan(glycome-db)', 'id': 'glytoucan.org/Structures/Glycans/G38695WE'}]} | 3 | {'taxid': 9913, 'name': 'Bos taurus', 'annotation_category': 'subsumption', 'evidence': [{'database': 'Subsumption', 'id': 'G75789AR', 'url': 'https://www.glygen.org/glycan/G75789AR'}], 'common_name': 'Bovine', 'glygen_name': 'Bovine', 'reference_species': 'Bos taurus [9913]'};{'taxid': 9606, 'name': 'Homo sapiens', 'a... | {'type': {'name': 'Human Milk Oligosaccharide'}, 'subtype': {'name': 'Other'}} | {'uniprot_canonical_ac': 'G5E897-1', 'xref_key': 'glycan_xref_sandbox', 'xref_id': 'G38695WE', 'protein_name': 'Protein O-glucosyltransferase 3', 'gene': 'Poglut3', 'gene_link': 'https://www.uniprot.org/uniprot/G5E897', 'tax_id': 10090, 'tax_name': 'Mus musculus', 'tax_common_name': 'Mouse', 'evidence': [{'id': 'G38695... | {'id': '491892627', 'url': 'https://pubchem.ncbi.nlm.nih.gov/substance/491892627', 'database': 'PubChem Substance', 'categories': ['Chemical']};{'id': '693', 'database': 'Glycosciences.de', 'categories': ['Discontinued']};{'id': '11002', 'url': 'https://www.genome.jp/dbget-bin/www_bget?carbbank+11002', 'database': 'Car... | 845.43 | {'gnome_glygen_oglycans': 'no', 'sandbox': 'yes', 'gnome_glygen': 'yes', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'no', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 656 | Saccharide | Hex(2)NeuGc(1) % 649.206542965 | freeEnd--?D-Glc--4b1D-Gal,p--3a2D-NeuGc,p$MONO,Und,0,0,freeEnd | null | {'related_accession': 'G03479FX', 'relationship': 'ancestor'};{'related_accession': 'G13697BC', 'relationship': 'ancestor'};{'related_accession': 'G15919RU', 'relationship': 'ancestor'};{'related_accession': 'G30664IS', 'relationship': 'ancestor'};{'related_accession': 'G64818UY', 'relationship': 'ancestor'};{'related_... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 1.5.36'} |
./raw_dataGS00002/snfg.svg | ./torsion_data/GS00002_torsion_data.txt | {'Cluster 0': {'count': 9366, '3_2_phi_mean': -73.02, '3_2_psi_mean': -134.09, '4_3_phi_mean': 72.99, '4_3_psi_mean': 78.83, '5_4_phi_mean': -70.7, '5_4_psi_mean': 117.5, '3_2_phi_std': 12.38, '3_2_psi_std': 39.16, '4_3_phi_std': 13.31, '4_3_psi_std': 16.65, '5_4_phi_std': 13.87, '5_4_psi_std': 41.47}, 'Cluster 1': {'c... | G77095CK | GS00002 | LFucpa1-2DGalpa1-3DGalpb1-3DGalpNAca1-OH | LFucpa1-2DGalpa1-3DGalpb1-3DGalpNAc | Fuc(a1-2)Gal(a1-3)Gal(b1-3)GalNAc | α-L-Fucp-(1→2)-α-D-Galp-(1→3)-β-D-Galp-(1→3)-D-GalNAc | WURCS=2.0/4,4,3/[u2112h_2*NCC/3=O][a2112h-1b_1-5][a2112h-1a_1-5][a1221m-1a_1-5]/1-2-3-4/a3-b1_b3-c1_c2-d1 | RES,1b:b-dgal-HEX-1:5,2s:n-acetyl,3b:b-dgal-HEX-1:5,4b:a-dgal-HEX-1:5,5b:a-lgal-HEX-1:5|6:d,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:3o(3+1)4d,4:4o(2+1)5d, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O[C@@H]4O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]4O)[C@H]2O)[C@@H](O)[C@H]1CO | null | 691.25 | null | Fuc(a1-2) | {'Gal': 2, 'Fuc': 1, 'GalNAc': 1} | {'Hex': 2, 'HexNAc': 1, 'dHex': 1} | 1 | 5 | 6 | 11.053462 | {'Cluster 0': 31.22, 'Cluster 1': 28.21, 'Cluster 2': 23.87, 'Cluster 3': 14.6, 'Cluster 4': 2.1} | {'Cluster 0': 63.317, 'Cluster 1': 7.2893, 'Cluster 2': 7.0693, 'Cluster 3': 3.3663, 'Cluster 4': 3.3263, 'Cluster 5': 3.1797, 'Cluster 6': 2.9397, 'Cluster 7': 2.853, 'Cluster 8': 1.8698, 'Cluster 9': 1.5365, 'Cluster 10': 1.2799, 'Cluster 11': 0.7166, 'Cluster 12': 0.5933, 'Cluster 13': 0.27, 'Cluster 14': 0.1866, 'C... | {'2': 0.2537120834159503, '3': 0.2651599701494174, '4': 0.26777415109045893, '5': 0.24875551102427657, '6': 0.22408953560954303, '7': 0.24197301306873847, '8': 0.2437292540567247} | {'0': [0, 11, 14], '1': [4, 9, 15], '2': [1, 3, 5, 7, 8], '3': [12, 13], '4': [2, 6, 10, 16]} | {'explained_variance_ratio': [0.1418408815585701, 0.09351406683349578, 0.08838750022371136, 0.055751077188687576, 0.046459786231526724, 0.040272697259682286, 0.03744849566150897, 0.03194154026759392, 0.024115711862323606, 0.021596411999106436], 'cumulative_variance': [0.1418408815585701, 0.2353549483920659, 0.323742448... | 1.5 | GROMACS | GLYCAM_06j | 300 | 1 | 200 | LFucpa1-2DGalpa1-3DGalpb1-3DGalpNAca1-OH | Fuc(a1-2)Gal(a1-3)Gal(b1-3)GalNAc(a1- | α-L-Fucp-(1→2)-α-D-Galp-(1→3)-β-D-Galp-(1→3)-α-D-GalpNAc-(1→ | G77945NE | WURCS=2.0/4,4,3/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a2112h-1a_1-5][a1221m-1a_1-5]/1-2-3-4/a3-b1_b3-c1_c2-d1 | LFucpa1-2DGalpa1-3DGalpb1-3DGalpNAcb1-OH | Fuc(a1-2)Gal(a1-3)Gal(b1-3)GalNAc(b1- | α-L-Fucp-(1→2)-α-D-Galp-(1→3)-β-D-Galp-(1→3)-β-D-GalpNAc-(1→ | G56973FQ | WURCS=2.0/4,4,3/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a2112h-1a_1-5][a1221m-1a_1-5]/1-2-3-4/a3-b1_b3-c1_c2-d1 | null | null | O-Glycan | {'GLA4-FUC5': {'2': {'phi': -63.41, 'psi': 105.27, 'strain': 1.678, 'linkage': '1-2'}, '3': {'phi': -78.39, 'psi': 90.7, 'strain': 1.215, 'linkage': '1-2'}, '4': {'phi': -59.6, 'psi': 141.11, 'strain': 1.49, 'linkage': '1-2'}, '5': {'phi': -78.84, 'psi': 96.76, 'strain': 1.215, 'linkage': '1-2'}, '6': {'phi': -64.61, '... | {'GLA4-FUC5': {'2': {'phi': -63.41, 'psi': 105.27, 'strain': 1.678, 'linkage': '1-2'}, '3': {'phi': -78.39, 'psi': 90.7, 'strain': 1.215, 'linkage': '1-2'}, '4': {'phi': -59.64, 'psi': 141.17, 'strain': 1.49, 'linkage': '1-2'}, '5': {'phi': -78.82, 'psi': 96.84, 'strain': 1.215, 'linkage': '1-2'}, '6': {'phi': -64.55, ... | {'GLA4-FUC5': {'2': {'phi': -63.41, 'psi': 105.27, 'strain': 1.678, 'linkage': '1-2'}, '3': {'phi': -78.39, 'psi': 90.7, 'strain': 1.215, 'linkage': '1-2'}, '4': {'phi': -59.6, 'psi': 141.11, 'strain': 1.49, 'linkage': '1-2'}, '5': {'phi': -78.84, 'psi': 96.76, 'strain': 1.215, 'linkage': '1-2'}, '6': {'phi': -64.61, '... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00003/snfg.svg | ./torsion_data/GS00003_torsion_data.txt | {'Cluster 0': {'count': 11086, '3_2_phi_mean': 67.7, '3_2_psi_mean': -141.64, '3_2_phi_std': 9.73, '3_2_psi_std': 66.21}, 'Cluster 1': {'count': 8079, '3_2_phi_mean': 76.32, '3_2_psi_mean': -138.76, '3_2_phi_std': 15.39, '3_2_psi_std': 59.96}, 'Cluster 2': {'count': 8054, '3_2_phi_mean': 77.09, '3_2_psi_mean': -142.89,... | G85977BN | GS00003 | DNeup5Aca2-6[DGalpNAca1-3]DGalpNAca1-OH | DNeup5Aca2-6[DGalpNAca1-3]DGalpNAc | GalNAc(a1-3)[Neu5Ac(a2-6)]GalNAc | α-D-GalpNAc-(1→3)[α-D-Neup5Ac-(2→6)]-D-GalNAc | WURCS=2.0/3,3,2/[u2112h_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2 | RES,1b:b-dgal-HEX-1:5,2s:n-acetyl,3b:a-dgal-HEX-1:5,4s:n-acetyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:3d(2+1)4n,4:1o(6+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2NC(C)=O)[C@@H](O)[C@H]1CO[C@]2(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O2 | null | 715.26 | {'motif': 'G00040MO', 'motif_label': 'O-Glycan core 5 fuzzy'} | Neu5Ac(a2-6);GalNAc(a1-3) | {'GalNAc': 2, 'Neu5Ac': 1} | {'HexNAc': 2, 'Neu5Ac': 1} | 13 | 13 | 19 | 10.464279 | {'Cluster 0': 27.71, 'Cluster 1': 20.2, 'Cluster 2': 20.13, 'Cluster 3': 18.73, 'Cluster 4': 13.23} | {'Cluster 0': 46.4104, 'Cluster 1': 12.5687, 'Cluster 2': 9.1891, 'Cluster 3': 7.1418, 'Cluster 4': 4.9895, 'Cluster 5': 4.662, 'Cluster 6': 3.8446, 'Cluster 7': 3.3747, 'Cluster 8': 2.9547, 'Cluster 9': 2.3498, 'Cluster 10': 0.8724, 'Cluster 11': 0.5149, 'Cluster 12': 0.445, 'Cluster 13': 0.3575, 'Cluster 14': 0.325} | {'2': 0.4686227974556124, '3': 0.2988471956608357, '4': 0.24801213879093045, '5': 0.2783127672079413, '6': 0.25708867871832825, '7': 0.2339921358372634, '8': 0.2574539160585065} | {'0': [0, 3, 6], '1': [1, 5, 7, 9], '2': [10], '3': [2, 11, 12, 14], '4': [4, 8, 13]} | {'explained_variance_ratio': [0.2389547987036773, 0.0899807017165907, 0.06834249441829354, 0.04706146684763711, 0.03309650589979163, 0.031016652260967163, 0.029469176108677646, 0.026696055443026598, 0.023095128137842594, 0.02279866205820332], 'cumulative_variance': [0.2389547987036773, 0.328935500420268, 0.397277994838... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | Neutralising only. | DNeup5Aca2-6[DGalpNAca1-3]DGalpNAca1-OH | GalNAc(a1-3)[Neu5Ac(a2-6)]GalNAc(a1- | α-D-GalpNAc-(1→3)[α-D-Neup5Ac-(2→6)]-α-D-GalpNAc-(1→ | G81016SV | WURCS=2.0/2,3,2/[a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2/a3-b1_a6-c2 | DNeup5Aca2-6[DGalpNAca1-3]DGalpNAcb1-OH | GalNAc(a1-3)[Neu5Ac(a2-6)]GalNAc(b1- | α-D-GalpNAc-(1→3)[α-D-Neup5Ac-(2→6)]-β-D-GalpNAc-(1→ | G47058RI | WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2 | null | null | null | {'A2G2-A2G3': {'2': {'phi': 69.23, 'psi': -152.46, 'strain': 0.974, 'linkage': '1-3'}, '3': {'phi': 74.9, 'psi': -148.15, 'strain': 0.806, 'linkage': '1-3'}, '4': {'phi': 68.45, 'psi': -153.96, 'strain': 0.974, 'linkage': '1-3'}, '5': {'phi': 66.99, 'psi': -147.75, 'strain': 0.979, 'linkage': '1-3'}, '6': {'phi': 86.13... | {'A2G2-A2G3': {'2': {'phi': 69.23, 'psi': -152.46, 'strain': 0.974, 'linkage': '1-3'}, '3': {'phi': 74.95, 'psi': -148.17, 'strain': 0.806, 'linkage': '1-3'}, '4': {'phi': 68.46, 'psi': -153.93, 'strain': 0.974, 'linkage': '1-3'}, '5': {'phi': 67.02, 'psi': -147.76, 'strain': 0.979, 'linkage': '1-3'}, '6': {'phi': 86.0... | {'A2G2-A2G3': {'2': {'phi': 69.23, 'psi': -152.46, 'strain': 0.974, 'linkage': '1-3'}, '3': {'phi': 74.9, 'psi': -148.15, 'strain': 0.806, 'linkage': '1-3'}, '4': {'phi': 68.45, 'psi': -153.96, 'strain': 0.974, 'linkage': '1-3'}, '5': {'phi': 66.99, 'psi': -147.75, 'strain': 0.979, 'linkage': '1-3'}, '6': {'phi': 86.13... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00004/snfg.svg | ./torsion_data/GS00004_torsion_data.txt | {'Cluster 0': {'count': 10918, '3_2_phi_mean': -76.58, '3_2_psi_mean': -144.26, '3_2_phi_std': 12.45, '3_2_psi_std': 55.25}, 'Cluster 1': {'count': 10688, '3_2_phi_mean': -76.85, '3_2_psi_mean': -149.12, '3_2_phi_std': 10.56, '3_2_psi_std': 50.51}, 'Cluster 2': {'count': 9481, '3_2_phi_mean': -76.25, '3_2_psi_mean': -1... | G71222KY | GS00004 | DNeup5Aca2-6[DGlcpNAcb1-3]DGalpNAca1-OH | DNeup5Aca2-6[DGlcpNAcb1-3]DGalpNAc | GlcNAc(b1-3)[Neu5Ac(a2-6)]GalNAc | β-D-GlcpNAc-(1→3)[α-D-Neup5Ac-(2→6)]-D-GalNAc | WURCS=2.0/3,3,2/[u2112h_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2 | RES,1b:b-dgal-HEX-1:5,2s:n-acetyl,3b:b-dglc-HEX-1:5,4s:n-acetyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:3d(2+1)4n,4:1o(6+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2NC(C)=O)[C@@H](O)[C@H]1CO[C@]2(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O2 | null | 715.26 | {'motif': 'G00036MO', 'motif_label': 'O-Glycan core 3 fuzzy'} | Neu5Ac(a2-6);GlcNAc(b1-3) | {'GlcNAc': 1, 'Neu5Ac': 1, 'GalNAc': 1} | {'HexNAc': 2, 'Neu5Ac': 1} | 13 | 13 | 19 | 9.959042 | {'Cluster 0': 27.29, 'Cluster 1': 26.72, 'Cluster 2': 23.7, 'Cluster 3': 16.72, 'Cluster 4': 5.57} | {'Cluster 0': 32.6742, 'Cluster 1': 31.1144, 'Cluster 2': 12.7462, 'Cluster 3': 8.7441, 'Cluster 4': 4.7745, 'Cluster 5': 2.4748, 'Cluster 6': 2.0973, 'Cluster 7': 1.9473, 'Cluster 8': 0.9524, 'Cluster 9': 0.7949, 'Cluster 10': 0.5899, 'Cluster 11': 0.5149, 'Cluster 12': 0.4675, 'Cluster 13': 0.1075} | {'2': 0.4982786578627117, '3': 0.42706458340012127, '4': 0.3952764653361819, '5': 0.41080011805518785, '6': 0.35845364388090806, '7': 0.37090449033413, '8': 0.38541893038860126} | {'0': [7], '1': [8, 9], '2': [2, 4, 5, 13], '3': [0, 11], '4': [1, 3, 6, 10, 12]} | {'explained_variance_ratio': [0.2612804911254766, 0.0955544944977664, 0.06636317709475165, 0.04032238817975529, 0.03325887604190297, 0.03021755748319266, 0.02757842082845966, 0.02701828301790658, 0.026020004293872554, 0.019535647710729295], 'cumulative_variance': [0.2612804911254766, 0.356834985623243, 0.42319816271799... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | Neutralising only. | DNeup5Aca2-6[DGlcpNAcb1-3]DGalpNAca1-OH | GlcNAc(b1-3)[Neu5Ac(a2-6)]GalNAc(a1- | β-D-GlcpNAc-(1→3)[α-D-Neup5Ac-(2→6)]-α-D-GalpNAc-(1→ | G63334FZ | WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2 | DNeup5Aca2-6[DGlcpNAcb1-3]DGalpNAcb1-OH | GlcNAc(b1-3)[Neu5Ac(a2-6)]GalNAc(b1- | β-D-GlcpNAc-(1→3)[α-D-Neup5Ac-(2→6)]-β-D-GalpNAc-(1→ | G11589YK | WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2 | null | null | null | {'A2G2-NAG3': {'2': {'phi': -69.91, 'psi': -150.21, 'strain': 1.139, 'linkage': '1-3'}, '3': {'phi': -85.85, 'psi': -154.64, 'strain': 0.668, 'linkage': '1-3'}, '4': {'phi': -85.69, 'psi': -121.33, 'strain': 1.249, 'linkage': '1-3'}, '5': {'phi': -81.89, 'psi': -128.65, 'strain': 1.249, 'linkage': '1-3'}, '6': {'phi': ... | {'A2G2-NAG3': {'2': {'phi': -69.91, 'psi': -150.21, 'strain': 1.139, 'linkage': '1-3'}, '3': {'phi': -85.86, 'psi': -154.62, 'strain': 0.668, 'linkage': '1-3'}, '4': {'phi': -85.69, 'psi': -121.34, 'strain': 1.249, 'linkage': '1-3'}, '5': {'phi': -81.86, 'psi': -128.7, 'strain': 1.249, 'linkage': '1-3'}, '6': {'phi': -... | {'A2G2-NAG3': {'2': {'phi': -69.91, 'psi': -150.21, 'strain': 1.139, 'linkage': '1-3'}, '3': {'phi': -85.85, 'psi': -154.64, 'strain': 0.668, 'linkage': '1-3'}, '4': {'phi': -85.69, 'psi': -121.33, 'strain': 1.249, 'linkage': '1-3'}, '5': {'phi': -81.89, 'psi': -128.65, 'strain': 1.249, 'linkage': '1-3'}, '6': {'phi': ... | null | 3 | {'taxid': 9913, 'name': 'Bos taurus', 'annotation_category': 'subsumption', 'evidence': [{'database': 'Subsumption', 'id': 'G63334FZ', 'url': 'https://www.glygen.org/glycan/G63334FZ'}, {'database': 'Subsumption', 'id': 'G77915WT', 'url': 'https://www.glygen.org/glycan/G77915WT'}], 'common_name': 'Bovine', 'glygen_name'... | {'type': {'name': 'O-linked'}, 'subtype': {'name': 'Core 3'}} | {'uniprot_canonical_ac': 'E5D8G1-1', 'xref_key': 'glycan_xref_sandbox', 'xref_id': 'G71222KY', 'protein_name': 'Polypeptide N-acetylgalactosaminyltransferase', 'gene': 'Galntl6', 'gene_link': 'https://www.uniprot.org/uniprot/E5D8G1', 'tax_id': 10090, 'tax_name': 'Mus musculus', 'tax_common_name': 'Mouse', 'evidence': [... | {'id': '491860908', 'url': 'https://pubchem.ncbi.nlm.nih.gov/substance/491860908', 'database': 'PubChem Substance', 'categories': ['Chemical']};{'id': 'G71222KY', 'url': 'https://glytoucan.org/Structures/Glycans/G71222KY', 'database': 'GlyTouCan', 'categories': ['Glycomics']};{'id': 'G71222KY', 'url': 'https://sandbox.... | 897.47 | {'gnome_glygen_oglycans': 'yes', 'sandbox': 'yes', 'gnome_glygen': 'yes', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'yes', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 656 | Saccharide | HexNAc(2)NeuAc(1) % 715.264726545 | freeEnd--?D-GalNAc(--3b1D-GlcNAc,p)--6a2D-NeuAc,p$MONO,Und,0,0,freeEnd | {'id': 'GGM.000035', 'name': '6-Sialyl-GalNAc', 'synonym': '6-Sialyl LN (type 1); 6-Sialyl LN (type 2)'} | {'related_accession': 'G60414ZR', 'relationship': 'ancestor'};{'related_accession': 'G68985JM', 'relationship': 'ancestor'};{'related_accession': 'G81915OX', 'relationship': 'ancestor'};{'related_accession': 'G83049TZ', 'relationship': 'ancestor'};{'related_accession': 'G81915OX', 'relationship': 'basecomposition'};{'r... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 2.0.3'} |
./raw_dataGS00005/snfg.svg | ./torsion_data/GS00005_torsion_data.txt | {'Cluster 0': {'count': 15228, '3_2_phi_mean': 76.84, '3_2_psi_mean': -143.14, '3_2_phi_std': 14.33, '3_2_psi_std': 36.61}, 'Cluster 1': {'count': 10535, '3_2_phi_mean': 71.23, '3_2_psi_mean': -145.59, '3_2_phi_std': 11.55, '3_2_psi_std': 40.16}, 'Cluster 2': {'count': 6855, '3_2_phi_mean': 84.17, '3_2_psi_mean': -136.... | G83524RP | GS00005 | DNeup5Aca2-6DGalpNAca1-3DGalpNAca1-OH | DNeup5Aca2-6DGalpNAca1-3DGalpNAc | Neu5Ac(a2-6)GalNAc(a1-3)GalNAc | α-D-Neup5Ac-(2→6)-α-D-GalpNAc-(1→3)-D-GalNAc | WURCS=2.0/3,3,2/[u2112h_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | RES,1b:b-dgal-HEX-1:5,2s:n-acetyl,3b:a-dgal-HEX-1:5,4s:n-acetyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:3d(2+1)4n,4:3o(6+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@H]2O[C@H](CO[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O3)[C@H](O)[C@H](O)[C@H]2NC(C)=O)[C@@H](O)[C@H]1CO | null | 715.26 | null | Neu5Ac(a2-6) | {'GalNAc': 2, 'Neu5Ac': 1} | {'HexNAc': 2, 'Neu5Ac': 1} | 1 | 5 | 6 | 10.437557 | {'Cluster 0': 38.07, 'Cluster 1': 26.34, 'Cluster 2': 17.14, 'Cluster 3': 11.86, 'Cluster 4': 6.59} | {'Cluster 0': 30.42, 'Cluster 1': 20.68, 'Cluster 2': 15.725, 'Cluster 3': 10.875, 'Cluster 4': 7.2025, 'Cluster 5': 3.79, 'Cluster 6': 2.6475, 'Cluster 7': 2.52, 'Cluster 8': 2.3025, 'Cluster 9': 1.0475, 'Cluster 10': 0.7925, 'Cluster 11': 0.7025, 'Cluster 12': 0.6325, 'Cluster 13': 0.5325, 'Cluster 14': 0.13} | {'2': 0.3187043996789221, '3': 0.31982210979292497, '4': 0.24633433675227917, '5': 0.2749426973049708, '6': 0.2895656265908472, '7': 0.2758491855439608, '8': 0.2546721962630322} | {'0': [0, 5, 9], '1': [4, 8], '2': [2, 12], '3': [3, 6, 11, 13], '4': [1, 7, 10, 14]} | {'explained_variance_ratio': [0.209367679156003, 0.08505551091479106, 0.06254711593947809, 0.05899771563749251, 0.04361091192273983, 0.03551842634033918, 0.02997687216352789, 0.02905833833936949, 0.024320594665724716, 0.021562685553891497], 'cumulative_variance': [0.209367679156003, 0.29442319007079404, 0.3569703060102... | 2 | AMBER | GLYCAM_06j | 300 | 1 | Neutralising only. | DNeup5Aca2-6DGalpNAca1-3DGalpNAca1-OH | Neu5Ac(a2-6)GalNAc(a1-3)GalNAc(a1- | α-D-Neup5Ac-(2→6)-α-D-GalpNAc-(1→3)-α-D-GalpNAc-(1→ | G90011PP | WURCS=2.0/2,3,2/[a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2/a3-b1_b6-c2 | DNeup5Aca2-6DGalpNAca1-3DGalpNAcb1-OH | Neu5Ac(a2-6)GalNAc(a1-3)GalNAc(b1- | α-D-Neup5Ac-(2→6)-α-D-GalpNAc-(1→3)-β-D-GalpNAc-(1→ | G22701RO | WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | null | null | null | {'A2G2-A2G3': {'2': {'phi': 69.33, 'psi': -151.76, 'strain': 0.974, 'linkage': '1-3'}, '3': {'phi': 76.6, 'psi': -158.92, 'strain': 1.254, 'linkage': '1-3'}, '4': {'phi': 99.28, 'psi': -146.54, 'strain': 1.994, 'linkage': '1-3'}, '5': {'phi': 60.08, 'psi': -150.42, 'strain': 0.974, 'linkage': '1-3'}, '6': {'phi': 64.26... | {'A2G2-A2G3': {'2': {'phi': 69.33, 'psi': -151.76, 'strain': 0.974, 'linkage': '1-3'}, '3': {'phi': 76.65, 'psi': -158.93, 'strain': 1.254, 'linkage': '1-3'}, '4': {'phi': 99.41, 'psi': -146.62, 'strain': 1.994, 'linkage': '1-3'}, '5': {'phi': 60.0, 'psi': -150.35, 'strain': 0.974, 'linkage': '1-3'}, '6': {'phi': 64.22... | {'A2G2-A2G3': {'2': {'phi': 69.33, 'psi': -151.76, 'strain': 0.974, 'linkage': '1-3'}, '3': {'phi': 76.6, 'psi': -158.92, 'strain': 1.254, 'linkage': '1-3'}, '4': {'phi': 99.28, 'psi': -146.54, 'strain': 1.994, 'linkage': '1-3'}, '5': {'phi': 60.08, 'psi': -150.42, 'strain': 0.974, 'linkage': '1-3'}, '6': {'phi': 64.26... | null | 3 | null | {'type': {'name': 'O-linked'}, 'subtype': {'name': 'Core 5'}} | {'uniprot_canonical_ac': 'E5D8G1-1', 'xref_key': 'glycan_xref_sandbox', 'xref_id': 'G83524RP', 'protein_name': 'Polypeptide N-acetylgalactosaminyltransferase', 'gene': 'Galntl6', 'gene_link': 'https://www.uniprot.org/uniprot/E5D8G1', 'tax_id': 10090, 'tax_name': 'Mus musculus', 'tax_common_name': 'Mouse', 'evidence': [... | {'id': 'G83524RP', 'url': 'https://glytoucan.org/Structures/Glycans/G83524RP', 'database': 'GlyTouCan', 'categories': ['Glycomics']};{'id': 'G83524RP', 'url': 'https://sandbox.glyomics.org/explore.html?G83524RP', 'database': 'SandBox', 'categories': ['Enzyme and Pathway']};{'id': 'G83524RP', 'url': 'https://gnome.glyom... | 897.47 | {'gnome_glygen_oglycans': 'yes', 'sandbox': 'yes', 'gnome_glygen': 'no', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'no', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 656 | Saccharide | HexNAc(2)NeuAc(1) % 715.264726545 | freeEnd--?D-GalNAc--3a1D-GalNAc,p--6a2D-NeuAc,p$MONO,Und,0,0,freeEnd | null | {'related_accession': 'G03155HR', 'relationship': 'ancestor'};{'related_accession': 'G07707ZV', 'relationship': 'ancestor'};{'related_accession': 'G17856AF', 'relationship': 'ancestor'};{'related_accession': 'G54095CK', 'relationship': 'ancestor'};{'related_accession': 'G68985JM', 'relationship': 'ancestor'};{'related_... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 2.8.1'} |
./raw_dataGS00006/snfg.svg | ./torsion_data/GS00006_torsion_data.txt | {'Cluster 0': {'count': 15278, '3_2_phi_mean': -69.55, '3_2_psi_mean': -117.95, '3_2_phi_std': 8.61, '3_2_psi_std': 14.79}, 'Cluster 1': {'count': 9783, '3_2_phi_mean': -70.36, '3_2_psi_mean': -124.77, '3_2_phi_std': 9.16, '3_2_psi_std': 18.61}, 'Cluster 2': {'count': 8399, '3_2_phi_mean': -72.99, '3_2_psi_mean': -110.... | G03213SR | GS00006 | DNeup5Aca2-6DGalpNAcb1-3DGlcpNAca1-OH | DNeup5Aca2-6DGalpNAcb1-3DGlcpNAc | Neu5Ac(a2-6)GalNAc(b1-3)GlcNAc | α-D-Neup5Ac-(2→6)-β-D-GalpNAc-(1→3)-D-GlcNAc | WURCS=2.0/3,3,2/[u2122h_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | RES,1b:b-dglc-HEX-1:5,2s:n-acetyl,3b:b-dgal-HEX-1:5,4s:n-acetyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:3d(2+1)4n,4:3o(6+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@@H]2O[C@H](CO[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O3)[C@H](O)[C@H](O)[C@H]2NC(C)=O)[C@H](O)[C@H]1CO | null | 715.26 | null | Neu5Ac(a2-6) | {'Neu5Ac': 1, 'GalNAc': 1, 'GlcNAc': 1} | {'HexNAc': 2, 'Neu5Ac': 1} | 1 | 5 | 6 | 9.663514 | {'Cluster 0': 38.2, 'Cluster 1': 24.46, 'Cluster 2': 21.0, 'Cluster 3': 8.97, 'Cluster 4': 7.38} | {'Cluster 0': 24.915, 'Cluster 1': 24.265, 'Cluster 2': 17.7225, 'Cluster 3': 11.3975, 'Cluster 4': 5.13, 'Cluster 5': 5.04, 'Cluster 6': 4.69, 'Cluster 7': 2.875, 'Cluster 8': 1.4675, 'Cluster 9': 1.07, 'Cluster 10': 0.6575, 'Cluster 11': 0.56, 'Cluster 12': 0.21} | {'2': 0.41220992253578836, '3': 0.3867448422078039, '4': 0.47778466254094837, '5': 0.48620588382521773, '6': 0.42305109431791316, '7': 0.41470319542392364, '8': 0.4158753045096378} | {'0': [4], '1': [3, 5, 6, 10], '2': [0, 7, 8, 12], '3': [2, 9], '4': [1, 11]} | {'explained_variance_ratio': [0.18747539396549934, 0.10725639656819443, 0.08836070217564834, 0.05739654436879192, 0.051356231829529815, 0.031687482616409364, 0.030511760938167987, 0.028065915226691492, 0.024058024775358105, 0.02121763731603428], 'cumulative_variance': [0.18747539396549934, 0.29473179053369375, 0.383092... | 2 | AMBER | GLYCAM_06j | 300 | 1 | Neutralising only. | DNeup5Aca2-6DGalpNAcb1-3DGlcpNAca1-OH | Neu5Ac(a2-6)GalNAc(b1-3)GlcNAc(a1- | α-D-Neup5Ac-(2→6)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1→ | G26133AM | WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | DNeup5Aca2-6DGalpNAcb1-3DGlcpNAcb1-OH | Neu5Ac(a2-6)GalNAc(b1-3)GlcNAc(b1- | α-D-Neup5Ac-(2→6)-β-D-GalpNAc-(1→3)-β-D-GlcpNAc-(1→ | G34742RW | WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | null | null | null | {'NDG2-GLC3': {'2': {'phi': -64.33, 'psi': -124.04, 'strain': 0.882, 'linkage': '1-3'}, '3': {'phi': -61.45, 'psi': -125.76, 'strain': 0.882, 'linkage': '1-3'}, '4': {'phi': -70.4, 'psi': -127.01, 'strain': 0.86, 'linkage': '1-3'}, '5': {'phi': -71.99, 'psi': -113.32, 'strain': 0.704, 'linkage': '1-3'}, '6': {'phi': -7... | {'NDG2-GLC3': {'2': {'phi': -64.33, 'psi': -124.04, 'strain': 0.882, 'linkage': '1-3'}, '3': {'phi': -61.39, 'psi': -125.83, 'strain': 0.882, 'linkage': '1-3'}, '4': {'phi': -70.4, 'psi': -126.98, 'strain': 0.86, 'linkage': '1-3'}, '5': {'phi': -71.96, 'psi': -113.33, 'strain': 0.704, 'linkage': '1-3'}, '6': {'phi': -7... | {'NDG2-GLC3': {'2': {'phi': -64.33, 'psi': -124.04, 'strain': 0.882, 'linkage': '1-3'}, '3': {'phi': -61.45, 'psi': -125.76, 'strain': 0.882, 'linkage': '1-3'}, '4': {'phi': -70.4, 'psi': -127.01, 'strain': 0.86, 'linkage': '1-3'}, '5': {'phi': -71.99, 'psi': -113.32, 'strain': 0.704, 'linkage': '1-3'}, '6': {'phi': -7... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00007/snfg.svg | ./torsion_data/GS00007_torsion_data.txt | {'Cluster 0': {'count': 12621, '3_2_phi_mean': -76.86, '3_2_psi_mean': 103.57, '3_2_phi_std': 18.05, '3_2_psi_std': 51.22}, 'Cluster 1': {'count': 9802, '3_2_phi_mean': -75.14, '3_2_psi_mean': 112.11, '3_2_phi_std': 21.9, '3_2_psi_std': 41.52}, 'Cluster 2': {'count': 6631, '3_2_phi_mean': -73.37, '3_2_psi_mean': 111.5,... | G94917JX | GS00007 | DNeup5Aca2-8DNeup5Gca2-3DGalpb1-4DGlcpa1-OH | DNeup5Aca2-8DNeup5Gca2-3DGalpb1-4DGlcp | Neu5Ac(a2-8)Neu5Gc(a2-3)Gal(b1-4)Glc | α-D-Neup5Ac-(2→8)-α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-D-Glc | WURCS=2.0/4,4,3/[u2122h][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a4-b1_b3-c2_c8-d2 | RES,1b:b-dglc-HEX-1:5,2b:b-dgal-HEX-1:5,3b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,4s:n-glycolyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1o(4+1)2d,2:2o(3+2)3d,3:3d(5+1)4n,4:3o(8+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](O)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(=O)CO)[C@H]([C@H](O)[C@H](O[C@]4(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O4)CO)O3)[C@H]2O)[C@H]1CO | null | 940.3 | null | Neu5Ac(a2-8) | {'Neu5Ac': 1, 'Neu5Gc': 1, 'Gal': 1, 'Glc': 1} | {'Hex': 2, 'Neu5Ac': 1, 'Neu5Gc': 1} | 19 | 19 | 28 | 10.707703 | {'Cluster 0': 31.55, 'Cluster 1': 24.5, 'Cluster 2': 16.58, 'Cluster 3': 14.34, 'Cluster 4': 13.03} | {'Cluster 0': 15.8734, 'Cluster 1': 14.2611, 'Cluster 2': 14.2386, 'Cluster 3': 11.3339, 'Cluster 4': 8.4167, 'Cluster 5': 8.2667, 'Cluster 6': 5.8944, 'Cluster 7': 4.4371, 'Cluster 8': 4.2771, 'Cluster 9': 3.8371, 'Cluster 10': 3.3347, 'Cluster 11': 1.8248, 'Cluster 12': 1.6848, 'Cluster 13': 1.1699, 'Cluster 14': 0.6... | {'2': 0.45535830804219324, '3': 0.3561065795330679, '4': 0.4060407130033886, '5': 0.3932355431472113, '6': 0.37844456367800405, '7': 0.38159005899729737, '8': 0.37053410852010754} | {'0': [3], '1': [4, 8], '2': [1, 7, 10], '3': [2, 5, 9, 12, 14], '4': [0, 6, 11, 13, 15]} | {'explained_variance_ratio': [0.21886712040169298, 0.08029024583929258, 0.07859610411262942, 0.06667138304990514, 0.04970547677638114, 0.034059708292307346, 0.025905789121971903, 0.02400529454986989, 0.02349105548365696, 0.019168852549304], 'cumulative_variance': [0.21886712040169298, 0.29915736624098554, 0.37775347035... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | 150 | DNeup5Aca2-8DNeup5Gca2-3DGalpb1-4DGlcpa1-OH | Neu5Ac(a2-8)Neu5Gc(a2-3)Gal(b1-4)Glc(a1- | α-D-Neup5Ac-(2→8)-α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-α-D-Glcp-(1→ | G83903NJ | WURCS=2.0/4,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a4-b1_b3-c2_c8-d2 | DNeup5Aca2-8DNeup5Gca2-3DGalpb1-4DGlcpb1-OH | Neu5Ac(a2-8)Neu5Gc(a2-3)Gal(b1-4)Glc(b1- | α-D-Neup5Ac-(2→8)-α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ | G27243GN | WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a4-b1_b3-c2_c8-d2 | null | null | null | {'GLC2-GAL3': {'2': {'phi': -76.72, 'psi': 106.6, 'strain': 0.169, 'linkage': '1-4'}, '3': {'phi': -67.11, 'psi': 114.93, 'strain': 0.16, 'linkage': '1-4'}, '4': {'phi': -80.1, 'psi': 82.54, 'strain': 1.192, 'linkage': '1-4'}, '5': {'phi': -68.19, 'psi': 150.85, 'strain': 2.077, 'linkage': '1-4'}, '6': {'phi': -65.54, ... | {'GLC2-GAL3': {'2': {'phi': -76.72, 'psi': 106.6, 'strain': 0.169, 'linkage': '1-4'}, '3': {'phi': -67.1, 'psi': 114.9, 'strain': 0.16, 'linkage': '1-4'}, '4': {'phi': -80.16, 'psi': 82.59, 'strain': 1.192, 'linkage': '1-4'}, '5': {'phi': -68.23, 'psi': 150.89, 'strain': 2.077, 'linkage': '1-4'}, '6': {'phi': -65.53, '... | {'GLC2-GAL3': {'2': {'phi': -76.72, 'psi': 106.6, 'strain': 0.169, 'linkage': '1-4'}, '3': {'phi': -67.11, 'psi': 114.93, 'strain': 0.16, 'linkage': '1-4'}, '4': {'phi': -80.1, 'psi': 82.54, 'strain': 1.192, 'linkage': '1-4'}, '5': {'phi': -68.19, 'psi': 150.85, 'strain': 2.077, 'linkage': '1-4'}, '6': {'phi': -65.54, ... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00008/snfg.svg | ./torsion_data/GS00008_torsion_data.txt | {'Cluster 0': {'count': 15132, '3_2_phi_mean': -76.54, '3_2_psi_mean': 108.48, '3_2_phi_std': 17.28, '3_2_psi_std': 42.25}, 'Cluster 1': {'count': 10559, '3_2_phi_mean': -75.6, '3_2_psi_mean': 114.08, '3_2_phi_std': 17.62, '3_2_psi_std': 26.83}, 'Cluster 2': {'count': 5317, '3_2_phi_mean': -75.84, '3_2_psi_mean': 112.1... | G33391ZV | GS00008 | DNeup5Gca2-8DNeup5Aca2-3DGalpb1-4DGlcpa1-OH | DNeup5Gca2-8DNeup5Aca2-3DGalpb1-4DGlcp | Neu5Gc(a2-8)Neu5Ac(a2-3)Gal(b1-4)Glc | α-D-Neup5Gc-(2→8)-α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)-D-Glc | WURCS=2.0/4,4,3/[u2122h][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3-4/a4-b1_b3-c2_c8-d2 | RES,1b:b-dglc-HEX-1:5,2b:b-dgal-HEX-1:5,3b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,4s:n-acetyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-glycolyl,LIN,1:1o(4+1)2d,2:2o(3+2)3d,3:3d(5+1)4n,4:3o(8+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](O)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O[C@]4(C(=O)O)C[C@H](O)[C@@H](NC(=O)CO)[C@H]([C@H](O)[C@H](O)CO)O4)CO)O3)[C@H]2O)[C@H]1CO | null | 940.3 | {'motif': 'G30207PZ', 'motif_label': 'GM4'} | Neu5Gc(a2-8) | {'Neu5Gc': 1, 'Neu5Ac': 1, 'Gal': 1, 'Glc': 1} | {'Hex': 2, 'Neu5Ac': 1, 'Neu5Gc': 1} | 19 | 19 | 28 | 10.553144 | {'Cluster 0': 37.83, 'Cluster 1': 26.39, 'Cluster 2': 13.29, 'Cluster 3': 11.98, 'Cluster 4': 10.51} | {'Cluster 0': 35.5239, 'Cluster 1': 10.9239, 'Cluster 2': 8.3967, 'Cluster 3': 7.8367, 'Cluster 4': 7.8092, 'Cluster 5': 7.2393, 'Cluster 6': 5.4695, 'Cluster 7': 3.8746, 'Cluster 8': 3.2872, 'Cluster 9': 2.7172, 'Cluster 10': 2.4198, 'Cluster 11': 1.9348, 'Cluster 12': 1.7273, 'Cluster 13': 0.5299, 'Cluster 14': 0.31} | {'2': 0.3812085952951624, '3': 0.3759715492608046, '4': 0.4089426322494262, '5': 0.40513575607239033, '6': 0.452127301043622, '7': 0.4060851458700137, '8': 0.38318710972970205} | {'0': [2, 13], '1': [3, 6, 12], '2': [0, 7, 10], '3': [1, 4, 5, 8, 9, 11], '4': [14]} | {'explained_variance_ratio': [0.2203073753279766, 0.08970044506989307, 0.06410881751091775, 0.055827312762647935, 0.0478239003184528, 0.034016096992532545, 0.02817376573536594, 0.022158615529525916, 0.021833201893690285, 0.02060482673233815], 'cumulative_variance': [0.2203073753279766, 0.31000782039786967, 0.3741166379... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | 150 | DNeup5Gca2-8DNeup5Aca2-3DGalpb1-4DGlcpa1-OH | Neu5Gc(a2-8)Neu5Ac(a2-3)Gal(b1-4)Glc(a1- | α-D-Neup5Gc-(2→8)-α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)-α-D-Glcp-(1→ | G24100LD | WURCS=2.0/4,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3-4/a4-b1_b3-c2_c8-d2 | DNeup5Gca2-8DNeup5Aca2-3DGalpb1-4DGlcpb1-OH | Neu5Gc(a2-8)Neu5Ac(a2-3)Gal(b1-4)Glc(b1- | α-D-Neup5Gc-(2→8)-α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ | G80829RZ | WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3-4/a4-b1_b3-c2_c8-d2 | null | null | null | {'GLC2-GAL3': {'2': {'phi': -80.06, 'psi': 115.6, 'strain': 0.5, 'linkage': '1-4'}, '3': {'phi': -59.84, 'psi': 107.62, 'strain': 1.494, 'linkage': '1-4'}, '4': {'phi': -85.43, 'psi': 117.21, 'strain': 0.5, 'linkage': '1-4'}, '5': {'phi': -69.72, 'psi': 120.32, 'strain': 0.031, 'linkage': '1-4'}, '6': {'phi': -76.88, '... | {'GLC2-GAL3': {'2': {'phi': -80.06, 'psi': 115.6, 'strain': 0.5, 'linkage': '1-4'}, '3': {'phi': -59.91, 'psi': 107.64, 'strain': 1.494, 'linkage': '1-4'}, '4': {'phi': -85.48, 'psi': 117.24, 'strain': 0.5, 'linkage': '1-4'}, '5': {'phi': -69.74, 'psi': 120.36, 'strain': 0.031, 'linkage': '1-4'}, '6': {'phi': -76.91, '... | {'GLC2-GAL3': {'2': {'phi': -80.06, 'psi': 115.6, 'strain': 0.5, 'linkage': '1-4'}, '3': {'phi': -59.84, 'psi': 107.62, 'strain': 1.494, 'linkage': '1-4'}, '4': {'phi': -85.43, 'psi': 117.21, 'strain': 0.5, 'linkage': '1-4'}, '5': {'phi': -69.72, 'psi': 120.32, 'strain': 0.031, 'linkage': '1-4'}, '6': {'phi': -76.88, '... | null | 4 | {'taxid': 9913, 'name': 'Bos taurus', 'annotation_category': 'subsumption', 'evidence': [{'database': 'Subsumption', 'id': 'G80829RZ', 'url': 'https://www.glygen.org/glycan/G80829RZ'}], 'common_name': 'Bovine', 'glygen_name': 'Bovine', 'reference_species': 'Bos taurus [9913]'};{'taxid': 9606, 'name': 'Homo sapiens', 'a... | {'type': {'name': 'Human Milk Oligosaccharide'}, 'subtype': {'name': 'Other'}} | {'uniprot_canonical_ac': 'G5E897-1', 'xref_key': 'glycan_xref_sandbox', 'xref_id': 'G33391ZV', 'protein_name': 'Protein O-glucosyltransferase 3', 'gene': 'Poglut3', 'gene_link': 'https://www.uniprot.org/uniprot/G5E897', 'tax_id': 10090, 'tax_name': 'Mus musculus', 'tax_common_name': 'Mouse', 'evidence': [{'id': 'G33391... | {'id': '491943499', 'url': 'https://pubchem.ncbi.nlm.nih.gov/substance/491943499', 'database': 'PubChem Substance', 'categories': ['Chemical']};{'id': 'G33391ZV', 'url': 'https://glytoucan.org/Structures/Glycans/G33391ZV', 'database': 'GlyTouCan', 'categories': ['Glycomics']};{'id': 'G33391ZV', 'url': 'https://sandbox.... | 1,206.6 | {'gnome_glygen_oglycans': 'no', 'sandbox': 'yes', 'gnome_glygen': 'yes', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'no', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 492 | Saccharide | Hex(2)NeuAc(1)NeuGc(1) % 940.3019596 | freeEnd--?D-Glc--4b1D-Gal,p--3a2D-NeuAc,p--8a2D-NeuGc,p$MONO,Und,0,0,freeEnd | null | {'related_accession': 'G22314RO', 'relationship': 'ancestor'};{'related_accession': 'G40099VD', 'relationship': 'ancestor'};{'related_accession': 'G87423KS', 'relationship': 'ancestor'};{'related_accession': 'G89606GV', 'relationship': 'ancestor'};{'related_accession': 'G40099VD', 'relationship': 'basecomposition'};{'r... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 2.0.3'} |
./raw_dataGS00009/snfg.svg | ./torsion_data/GS00009_torsion_data.txt | {'Cluster 0': {'count': 12833, '3_2_phi_mean': -76.04, '3_2_psi_mean': 114.34, '3_2_phi_std': 15.35, '3_2_psi_std': 29.53}, 'Cluster 1': {'count': 10123, '3_2_phi_mean': -75.3, '3_2_psi_mean': 116.42, '3_2_phi_std': 16.6, '3_2_psi_std': 29.39}, 'Cluster 2': {'count': 9283, '3_2_phi_mean': -76.13, '3_2_psi_mean': 114.11... | G08380SA | GS00009 | DNeup5Gca2-8DNeup5Gca2-3DGalpb1-4DGlcpa1-OH | DNeup5Gca2-8DNeup5Gca2-3DGalpb1-4DGlcp | Neu5Gc(a2-8)Neu5Gc(a2-3)Gal(b1-4)Glc | α-D-Neup5Gc-(2→8)-α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-D-Glc | WURCS=2.0/3,4,3/[u2122h][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3-3/a4-b1_b3-c2_c8-d2 | RES,1b:b-dglc-HEX-1:5,2b:b-dgal-HEX-1:5,3b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,4s:n-glycolyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-glycolyl,LIN,1:1o(4+1)2d,2:2o(3+2)3d,3:3d(5+1)4n,4:3o(8+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](O)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(=O)CO)[C@H]([C@H](O)[C@H](O[C@]4(C(=O)O)C[C@H](O)[C@@H](NC(=O)CO)[C@H]([C@H](O)[C@H](O)CO)O4)CO)O3)[C@H]2O)[C@H]1CO | null | 956.3 | null | Neu5Gc(a2-8) | {'Neu5Gc': 2, 'Gal': 1, 'Glc': 1} | {'Hex': 2, 'Neu5Gc': 2} | 20 | 20 | 29 | 10.805481 | {'Cluster 0': 32.08, 'Cluster 1': 25.3, 'Cluster 2': 23.21, 'Cluster 3': 11.69, 'Cluster 4': 7.72} | {'Cluster 0': 27.8822, 'Cluster 1': 17.0908, 'Cluster 2': 11.6163, 'Cluster 3': 10.034, 'Cluster 4': 7.3418, 'Cluster 5': 6.3744, 'Cluster 6': 4.5595, 'Cluster 7': 3.4872, 'Cluster 8': 3.0547, 'Cluster 9': 2.2748, 'Cluster 10': 2.1323, 'Cluster 11': 1.3099, 'Cluster 12': 1.1799, 'Cluster 13': 1.0924, 'Cluster 14': 0.39... | {'2': 0.4235400195221006, '3': 0.46440162389493395, '4': 0.38424521358320973, '5': 0.3357896686176932, '6': 0.4025939836546814, '7': 0.34528738901105505, '8': 0.3583959188489479} | {'0': [6, 9], '1': [5, 7], '2': [1, 8, 13, 15], '3': [0, 3, 4, 12], '4': [2, 10, 11, 14]} | {'explained_variance_ratio': [0.2033782024129014, 0.1103692768641323, 0.07622869773395007, 0.06283938040490102, 0.03359856153487094, 0.03158493250806797, 0.025839756056870736, 0.023345760655439574, 0.02067505233550986, 0.01953012384465586], 'cumulative_variance': [0.2033782024129014, 0.31374747927703367, 0.389976177010... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | 150 | DNeup5Gca2-8DNeup5Gca2-3DGalpb1-4DGlcpa1-OH | Neu5Gc(a2-8)Neu5Gc(a2-3)Gal(b1-4)Glc(a1- | α-D-Neup5Gc-(2→8)-α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-α-D-Glcp-(1→ | G85971RS | WURCS=2.0/3,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3-3/a4-b1_b3-c2_c8-d2 | DNeup5Gca2-8DNeup5Gca2-3DGalpb1-4DGlcpb1-OH | Neu5Gc(a2-8)Neu5Gc(a2-3)Gal(b1-4)Glc(b1- | α-D-Neup5Gc-(2→8)-α-D-Neup5Gc-(2→3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ | G84891DZ | WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3-3/a4-b1_b3-c2_c8-d2 | null | null | null | {'GLC2-GAL3': {'2': {'phi': -69.95, 'psi': 117.22, 'strain': 0.16, 'linkage': '1-4'}, '3': {'phi': -91.46, 'psi': 114.66, 'strain': 1.523, 'linkage': '1-4'}, '4': {'phi': -73.58, 'psi': 116.61, 'strain': -0.0, 'linkage': '1-4'}, '5': {'phi': -81.0, 'psi': 127.47, 'strain': 0.775, 'linkage': '1-4'}, '6': {'phi': -84.56,... | {'GLC2-GAL3': {'2': {'phi': -69.95, 'psi': 117.22, 'strain': 0.16, 'linkage': '1-4'}, '3': {'phi': -91.48, 'psi': 114.68, 'strain': 1.523, 'linkage': '1-4'}, '4': {'phi': -73.64, 'psi': 116.62, 'strain': -0.0, 'linkage': '1-4'}, '5': {'phi': -81.05, 'psi': 127.51, 'strain': 0.775, 'linkage': '1-4'}, '6': {'phi': -84.54... | {'GLC2-GAL3': {'2': {'phi': -69.95, 'psi': 117.22, 'strain': 0.16, 'linkage': '1-4'}, '3': {'phi': -91.46, 'psi': 114.66, 'strain': 1.523, 'linkage': '1-4'}, '4': {'phi': -73.58, 'psi': 116.61, 'strain': -0.0, 'linkage': '1-4'}, '5': {'phi': -81.0, 'psi': 127.47, 'strain': 0.775, 'linkage': '1-4'}, '6': {'phi': -84.56,... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00010/snfg.svg | ./torsion_data/GS00010_torsion_data.txt | {'Cluster 0': {'count': 11181, '3_2_phi_mean': -75.28, '3_2_psi_mean': 116.66, '4_3_phi_mean': 72.48, '4_3_psi_mean': 86.62, '5_4_phi_mean': -85.59, '5_4_psi_mean': -136.85, '3_2_phi_std': 14.3, '3_2_psi_std': 18.27, '4_3_phi_std': 15.85, '4_3_psi_std': 27.03, '5_4_phi_std': 13.06, '5_4_psi_std': 61.34}, 'Cluster 1': {... | G00012MO | GS00010 | DGalpNAcb1-3DGalpa1-3DGalpb1-4DGlcpa1-OH | DGalpNAcb1-3DGalpa1-3DGalpb1-4DGlcp | GalNAc(b1-3)Gal(a1-3)Gal(b1-4)Glc | β-D-GalpNAc-(1→3)-α-D-Galp-(1→3)-β-D-Galp-(1→4)-D-Glc | WURCS=2.0/4,4,3/[u2122h][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b3-c1_c3-d1 | RES,1b:b-dglc-HEX-1:5,2b:b-dgal-HEX-1:5,3b:a-dgal-HEX-1:5,4b:b-dgal-HEX-1:5,5s:n-acetyl,LIN,1:1o(4+1)2d,2:2o(3+1)3d,3:3o(3+1)4d,4:4d(2+1)5n, | O1C(O)[C@H](O)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@H]3O[C@H](CO)[C@H](O)[C@H](O[C@@H]4O[C@H](CO)[C@H](O)[C@H](O)[C@H]4NC(C)=O)[C@H]3O)[C@H]2O)[C@H]1CO | null | 707.25 | {'motif': 'G24432YB', 'motif_label': 'a-Gal antigen'} | GalNAc(b1-3) | {'Gal': 2, 'GalNAc': 1, 'Glc': 1} | {'Hex': 3, 'HexNAc': 1} | 11 | 14 | 21 | 10.390486 | {'Cluster 0': 37.27, 'Cluster 1': 25.65, 'Cluster 2': 17.4, 'Cluster 3': 16.64, 'Cluster 4': 3.04} | {'Cluster 0': 25.8, 'Cluster 1': 22.3833, 'Cluster 2': 14.3167, 'Cluster 3': 12.16, 'Cluster 4': 8.9933, 'Cluster 5': 7.0067, 'Cluster 6': 2.5067, 'Cluster 7': 2.3967, 'Cluster 8': 2.1233, 'Cluster 9': 1.0833, 'Cluster 10': 0.77, 'Cluster 11': 0.2, 'Cluster 12': 0.1833, 'Cluster 13': 0.0733, 'Cluster 14': 0.0033} | {'2': 0.40993027587801945, '3': 0.28753618251065116, '4': 0.3025062624418661, '5': 0.22931115531130314, '6': 0.22611579506782156, '7': 0.202274876710624, '8': 0.20400928923661882} | {'0': [], '1': [4, 13, 14], '2': [1, 2, 3, 6, 8, 9, 11], '3': [0, 7, 12], '4': [5, 10]} | {'explained_variance_ratio': [0.13112974693516286, 0.10503144186892395, 0.09688326267273123, 0.07670297555477293, 0.06164829882313905, 0.035725517627707086, 0.03125369957377917, 0.023774253976859894, 0.023091782329564388, 0.022434123782899], 'cumulative_variance': [0.13112974693516286, 0.23616118880408682, 0.3330444514... | 1.5 | AMBER | GLYCAM_06j | 300 | 1 | 150 | DGalpNAcb1-3DGalpa1-3DGalpb1-4DGlcpa1-OH | GalNAc(b1-3)Gal(a1-3)Gal(b1-4)Glc(a1- | β-D-GalpNAc-(1→3)-α-D-Galp-(1→3)-β-D-Galp-(1→4)-α-D-Glcp-(1→ | G54440EA | WURCS=2.0/4,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b3-c1_c3-d1 | DGalpNAcb1-3DGalpa1-3DGalpb1-4DGlcpb1-OH | GalNAc(b1-3)Gal(a1-3)Gal(b1-4)Glc(b1- | β-D-GalpNAc-(1→3)-α-D-Galp-(1→3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ | G57710SU | WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b3-c1_c3-d1 | null | null | null | {'GAL3-GLA4': {'2': {'phi': 67.26, 'psi': -171.66, 'strain': 1.618, 'linkage': '1-3'}, '3': {'phi': 58.81, 'psi': -151.95, 'strain': 1.506, 'linkage': '1-3'}, '4': {'phi': 81.04, 'psi': -88.25, 'strain': 1.349, 'linkage': '1-3'}, '5': {'phi': 58.66, 'psi': -134.66, 'strain': 1.819, 'linkage': '1-3'}, '6': {'phi': 73.1,... | {'GAL3-GLA4': {'2': {'phi': 67.26, 'psi': -171.66, 'strain': 1.618, 'linkage': '1-3'}, '3': {'phi': 58.87, 'psi': -151.94, 'strain': 1.506, 'linkage': '1-3'}, '4': {'phi': 81.01, 'psi': -88.27, 'strain': 1.349, 'linkage': '1-3'}, '5': {'phi': 58.74, 'psi': -134.69, 'strain': 1.819, 'linkage': '1-3'}, '6': {'phi': 73.06... | {'GAL3-GLA4': {'2': {'phi': 67.26, 'psi': -171.66, 'strain': 1.618, 'linkage': '1-3'}, '3': {'phi': 58.81, 'psi': -151.95, 'strain': 1.506, 'linkage': '1-3'}, '4': {'phi': 81.04, 'psi': -88.25, 'strain': 1.349, 'linkage': '1-3'}, '5': {'phi': 58.66, 'psi': -134.66, 'strain': 1.819, 'linkage': '1-3'}, '6': {'phi': 73.1,... | null | 4 | {'taxid': 9606, 'name': 'Homo sapiens', 'annotation_category': 'subsumption', 'evidence': [{'database': 'Subsumption', 'id': 'G57710SU', 'url': 'https://www.glygen.org/glycan/G57710SU'}], 'common_name': 'Human', 'glygen_name': 'Human', 'reference_species': 'Homo sapiens [9606]'};{'taxid': 10090, 'name': 'Mus musculus',... | {'type': {'name': 'Glycosphingolipid'}, 'subtype': {'name': 'Isoglobo series'}} | {'uniprot_canonical_ac': 'G5E897-1', 'xref_key': 'glycan_xref_sandbox', 'xref_id': 'G00012MO', 'protein_name': 'Protein O-glucosyltransferase 3', 'gene': 'Poglut3', 'gene_link': 'https://www.uniprot.org/uniprot/G5E897', 'tax_id': 10090, 'tax_name': 'Mus musculus', 'tax_common_name': 'Mouse', 'evidence': [{'id': 'G00012... | {'id': '491870200', 'url': 'https://pubchem.ncbi.nlm.nih.gov/substance/491870200', 'database': 'PubChem Substance', 'categories': ['Chemical']};{'id': '4097', 'database': 'Glycosciences.de', 'categories': ['Discontinued']};{'id': '15855', 'url': 'https://www.genome.jp/dbget-bin/www_bget?carbbank+15855', 'database': 'Ca... | 903.47 | {'gnome_glygen_oglycans': 'no', 'sandbox': 'yes', 'gnome_glygen': 'yes', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'no', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 492 | Saccharide | HexNAc(1)Hex(3) % 707.248407805 | freeEnd--?D-Glc--4b1D-Gal,p--3a1D-Gal,p--3b1D-GalNAc,p$MONO,Und,0,0,freeEnd | {'id': 'GGM.000015', 'name': 'a-Gal antigen', 'synonym': 'alpha-Gal antigen'};{'id': 'GGM.000071', 'name': 'Isoglobotetraosylceramide', 'keywords': 'Glycolipid'};{'id': 'GGM.000083', 'name': 'Cytolipin R', 'keywords': 'Glycolipid'} | {'related_accession': 'G04811WK', 'relationship': 'ancestor'};{'related_accession': 'G08590QR', 'relationship': 'ancestor'};{'related_accession': 'G15216HY', 'relationship': 'ancestor'};{'related_accession': 'G29964CE', 'relationship': 'ancestor'};{'related_accession': 'G33233SN', 'relationship': 'ancestor'};{'related_... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 1.0.13'} |
./raw_dataGS00011/snfg.svg | ./torsion_data/GS00011_torsion_data.txt | {'Cluster 0': {'count': 13624, '3_2_phi_mean': -76.75, '3_2_psi_mean': 113.26, '4_3_phi_mean': 83.51, '4_3_psi_mean': 126.69, '3_2_phi_std': 16.75, '3_2_psi_std': 37.52, '4_3_phi_std': 13.36, '4_3_psi_std': 26.17}, 'Cluster 1': {'count': 12088, '3_2_phi_mean': -78.09, '3_2_psi_mean': 116.33, '4_3_phi_mean': 80.76, '4_3... | G37525EU | GS00011 | DNeup5Aca2-3DGalpa1-4DGalpb1-4DGlcpa1-OH | DNeup5Aca2-3DGalpa1-4DGalpb1-4DGlcp | Neu5Ac(a2-3)Gal(a1-4)Gal(b1-4)Glc | α-D-Neup5Ac-(2→3)-α-D-Galp-(1→4)-β-D-Galp-(1→4)-D-Glc | WURCS=2.0/4,4,3/[u2122h][a2112h-1b_1-5][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a4-b1_b4-c1_c3-d2 | RES,1b:b-dglc-HEX-1:5,2b:b-dgal-HEX-1:5,3b:a-dgal-HEX-1:5,4b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,5s:n-acetyl,LIN,1:1o(4+1)2d,2:2o(4+1)3d,3:3o(3+2)4d,4:4d(5+1)5n, | O1C(O)[C@H](O)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O[C@H]3O[C@H](CO)[C@H](O)[C@H](O[C@]4(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O4)[C@H]3O)[C@H](O)[C@H]2O)[C@H]1CO | null | 795.26 | null | Neu5Ac(a2-3) | {'Gal': 2, 'Neu5Ac': 1, 'Glc': 1} | {'Hex': 3, 'Neu5Ac': 1} | 14 | 16 | 24 | 10.722626 | {'Cluster 0': 34.06, 'Cluster 1': 30.22, 'Cluster 2': 12.45, 'Cluster 3': 12.31, 'Cluster 4': 10.96} | {'Cluster 0': 27.5175, 'Cluster 1': 26.4025, 'Cluster 2': 8.135, 'Cluster 3': 7.255, 'Cluster 4': 6.6575, 'Cluster 5': 6.58, 'Cluster 6': 6.265, 'Cluster 7': 2.48, 'Cluster 8': 2.215, 'Cluster 9': 1.605, 'Cluster 10': 1.355, 'Cluster 11': 0.94, 'Cluster 12': 0.8575, 'Cluster 13': 0.695, 'Cluster 14': 0.5725, 'Cluster 1... | {'2': 0.42376110302451864, '3': 0.29754185841183617, '4': 0.27662381608757364, '5': 0.2622343132673724, '6': 0.26087824175966834, '7': 0.2704642991749054, '8': 0.2724786376767135} | {'0': [0, 5, 8, 10, 15], '1': [3, 14], '2': [2, 9, 12], '3': [1, 4, 13], '4': [6, 7, 11]} | {'explained_variance_ratio': [0.15774632224823995, 0.13324674706453693, 0.07505125593922327, 0.055367361342985304, 0.048066599755190856, 0.04014059317445401, 0.03245912593533754, 0.02937684562757932, 0.022001264742014862, 0.020874536097758502], 'cumulative_variance': [0.15774632224823995, 0.2909930693127769, 0.36604432... | 1.5 | AMBER | GLYCAM_06j | 300 | 1 | 150 | DNeup5Aca2-3DGalpa1-4DGalpb1-4DGlcpa1-OH | Neu5Ac(a2-3)Gal(a1-4)Gal(b1-4)Glc(a1- | α-D-Neup5Ac-(2→3)-α-D-Galp-(1→4)-β-D-Galp-(1→4)-α-D-Glcp-(1→ | G31192AQ | WURCS=2.0/4,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a4-b1_b4-c1_c3-d2 | DNeup5Aca2-3DGalpa1-4DGalpb1-4DGlcpb1-OH | Neu5Ac(a2-3)Gal(a1-4)Gal(b1-4)Glc(b1- | α-D-Neup5Ac-(2→3)-α-D-Galp-(1→4)-β-D-Galp-(1→4)-β-D-Glcp-(1→ | G88815RG | WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a4-b1_b4-c1_c3-d2 | null | null | null | {'GLC2-GAL3': {'2': {'phi': -80.68, 'psi': 124.59, 'strain': 0.775, 'linkage': '1-4'}, '3': {'phi': -70.49, 'psi': 128.71, 'strain': 0.008, 'linkage': '1-4'}, '4': {'phi': -80.38, 'psi': 136.68, 'strain': 0.987, 'linkage': '1-4'}, '5': {'phi': -68.61, 'psi': 112.42, 'strain': 0.16, 'linkage': '1-4'}, '6': {'phi': -66.2... | {'GLC2-GAL3': {'2': {'phi': -80.68, 'psi': 124.59, 'strain': 0.775, 'linkage': '1-4'}, '3': {'phi': -70.46, 'psi': 128.7, 'strain': 0.008, 'linkage': '1-4'}, '4': {'phi': -80.33, 'psi': 136.64, 'strain': 0.987, 'linkage': '1-4'}, '5': {'phi': -68.62, 'psi': 112.42, 'strain': 0.16, 'linkage': '1-4'}, '6': {'phi': -66.34... | {'GLC2-GAL3': {'2': {'phi': -80.68, 'psi': 124.59, 'strain': 0.775, 'linkage': '1-4'}, '3': {'phi': -70.49, 'psi': 128.71, 'strain': 0.008, 'linkage': '1-4'}, '4': {'phi': -80.38, 'psi': 136.68, 'strain': 0.987, 'linkage': '1-4'}, '5': {'phi': -68.61, 'psi': 112.42, 'strain': 0.16, 'linkage': '1-4'}, '6': {'phi': -66.2... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00012/snfg.svg | ./torsion_data/GS00012_torsion_data.txt | {'Cluster 0': {'count': 16162, '3_2_phi_mean': 87.28, '3_2_psi_mean': -124.63, '3_2_phi_std': 17.22, '3_2_psi_std': 26.01}, 'Cluster 1': {'count': 10609, '3_2_phi_mean': 71.3, '3_2_psi_mean': -143.4, '3_2_phi_std': 11.77, '3_2_psi_std': 13.37}, 'Cluster 2': {'count': 5847, '3_2_phi_mean': 97.51, '3_2_psi_mean': -108.65... | G18712XX | GS00012 | DNeup5Aca2-6DGalpNAca1-3DGlcpNAca1-OH | DNeup5Aca2-6DGalpNAca1-3DGlcpNAc | Neu5Ac(a2-6)GalNAc(a1-3)GlcNAc | α-D-Neup5Ac-(2→6)-α-D-GalpNAc-(1→3)-D-GlcNAc | WURCS=2.0/3,3,2/[u2122h_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | RES,1b:b-dglc-HEX-1:5,2s:n-acetyl,3b:a-dgal-HEX-1:5,4s:n-acetyl,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:3d(2+1)4n,4:3o(6+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@H]2O[C@H](CO[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O3)[C@H](O)[C@H](O)[C@H]2NC(C)=O)[C@H](O)[C@H]1CO | null | 715.26 | null | Neu5Ac(a2-6) | {'Neu5Ac': 1, 'GalNAc': 1, 'GlcNAc': 1} | {'HexNAc': 2, 'Neu5Ac': 1} | 1 | 5 | 6 | 9.953737 | {'Cluster 0': 40.41, 'Cluster 1': 26.52, 'Cluster 2': 14.62, 'Cluster 3': 12.53, 'Cluster 4': 5.93} | {'Cluster 0': 30.445, 'Cluster 1': 24.6525, 'Cluster 2': 18.84, 'Cluster 3': 9.76, 'Cluster 4': 3.52, 'Cluster 5': 3.255, 'Cluster 6': 2.61, 'Cluster 7': 2.335, 'Cluster 8': 1.39, 'Cluster 9': 1.0525, 'Cluster 10': 0.95, 'Cluster 11': 0.63, 'Cluster 12': 0.4775, 'Cluster 13': 0.0825} | {'2': 0.43802846729829314, '3': 0.43168473891307074, '4': 0.45643334140423014, '5': 0.3853843908691513, '6': 0.28814897826772934, '7': 0.29404207313112773, '8': 0.3470734904603066} | {'0': [8], '1': [0], '2': [2, 5, 9], '3': [1, 3, 6, 7, 10, 12, 13], '4': [4, 11]} | {'explained_variance_ratio': [0.18303653862101327, 0.09809360600146419, 0.08098267698865445, 0.057904579686617455, 0.04890639028455224, 0.0324673593220714, 0.031907719894417624, 0.030066622659402725, 0.027360951236409033, 0.02070132122685705], 'cumulative_variance': [0.18303653862101327, 0.28113014462247743, 0.36211282... | 2 | AMBER | GLYCAM_06j | 300 | 1 | Neutralising only. | DNeup5Aca2-6DGalpNAca1-3DGlcpNAca1-OH | Neu5Ac(a2-6)GalNAc(a1-3)GlcNAc(a1- | α-D-Neup5Ac-(2→6)-α-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1→ | G92980RJ | WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | DNeup5Aca2-6DGalpNAca1-3DGlcpNAcb1-OH | Neu5Ac(a2-6)GalNAc(a1-3)GlcNAc(b1- | α-D-Neup5Ac-(2→6)-α-D-GalpNAc-(1→3)-β-D-GlcpNAc-(1→ | G56098KF | WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b6-c2 | null | null | null | {'NDG2-A2G3': {'2': {'phi': 74.18, 'psi': -141.15, 'strain': 0.806, 'linkage': '1-3'}, '3': {'phi': 78.24, 'psi': -146.06, 'strain': 0.806, 'linkage': '1-3'}, '4': {'phi': 107.23, 'psi': -115.73, 'strain': 2.778, 'linkage': '1-3'}, '5': {'phi': 70.86, 'psi': 168.66, 'strain': 2.555, 'linkage': '1-3'}, '6': {'phi': 60.5... | {'NDG2-A2G3': {'2': {'phi': 74.18, 'psi': -141.15, 'strain': 0.806, 'linkage': '1-3'}, '3': {'phi': 78.26, 'psi': -146.08, 'strain': 0.806, 'linkage': '1-3'}, '4': {'phi': 107.22, 'psi': -115.7, 'strain': 2.778, 'linkage': '1-3'}, '5': {'phi': 70.83, 'psi': 168.68, 'strain': 2.555, 'linkage': '1-3'}, '6': {'phi': 60.55... | {'NDG2-A2G3': {'2': {'phi': 74.18, 'psi': -141.15, 'strain': 0.806, 'linkage': '1-3'}, '3': {'phi': 78.24, 'psi': -146.06, 'strain': 0.806, 'linkage': '1-3'}, '4': {'phi': 107.23, 'psi': -115.73, 'strain': 2.778, 'linkage': '1-3'}, '5': {'phi': 70.86, 'psi': 168.66, 'strain': 2.555, 'linkage': '1-3'}, '6': {'phi': 60.5... | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null |
./raw_dataGS00013/snfg.svg | ./torsion_data/GS00013_torsion_data.txt | {'Cluster 0': {'count': 10281, '3_2_phi_mean': -69.27, '3_2_psi_mean': 88.47, '3_2_phi_std': 7.72, '3_2_psi_std': 11.99}, 'Cluster 1': {'count': 8539, '3_2_phi_mean': -68.32, '3_2_psi_mean': 87.45, '3_2_phi_std': 6.75, '3_2_psi_std': 11.45}, 'Cluster 2': {'count': 5873, '3_2_phi_mean': -80.37, '3_2_psi_mean': 84.93, '3... | G67189MD | GS00013 | LFucpa1-2DGalpa1-OH | LFucpa1-2DGalp | Fuc(a1-2)Gal | α-L-Fucp-(1→2)-D-Gal | WURCS=2.0/2,2,1/[u2112h][a1221m-1a_1-5]/1-2/a2-b1 | RES,1b:b-dgal-HEX-1:5,2b:a-lgal-HEX-1:5|6:d,LIN,1:1o(2+1)2d, | O1C(O)[C@H](O[C@@H]2O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H](O)[C@H]1CO | null | 326.12 | null | Fuc(a1-2) | {'Fuc': 1, 'Gal': 1} | {'Hex': 1, 'dHex': 1} | 3 | 7 | 10 | 8.698426 | {'Cluster 0': 34.27, 'Cluster 1': 28.46, 'Cluster 2': 19.57, 'Cluster 3': 15.7, 'Cluster 4': 2.0} | {'Cluster 0': 63.3803, 'Cluster 1': 15.2385, 'Cluster 2': 9.2791, 'Cluster 3': 5.0962, 'Cluster 4': 2.4931, 'Cluster 5': 1.3799, 'Cluster 6': 1.3032, 'Cluster 7': 0.9099, 'Cluster 8': 0.7233, 'Cluster 9': 0.18, 'Cluster 10': 0.0167} | {'2': 0.4249255382631574, '3': 0.26281268693894266, '4': 0.23031430198374891, '5': 0.2439154464126305, '6': 0.22864265991314695, '7': 0.2322229067041486, '8': 0.218628818204185} | {'0': [7], '1': [1, 5, 6], '2': [2, 3], '3': [4, 10], '4': [0, 8, 9]} | {'explained_variance_ratio': [0.16587853751661044, 0.10072041856418106, 0.07742278111713417, 0.04368083475097823, 0.03869150533182649, 0.03189845139493971, 0.030206164001552363, 0.026288961300730284, 0.025836336613480764, 0.024024996724937804], 'cumulative_variance': [0.16587853751661044, 0.2665989560807915, 0.34402173... | 1.5 | GROMACS | GLYCAM_06j | 300 | 1 | 150 | LFucpa1-2DGalpa1-OH | Fuc(a1-2)Gal(a1- | α-L-Fucp-(1→2)-α-D-Galp-(1→ | G37862DQ | WURCS=2.0/2,2,1/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2/a2-b1 | LFucpa1-2DGalpb1-OH | Fuc(a1-2)Gal(b1- | α-L-Fucp-(1→2)-β-D-Galp-(1→ | G00068MO | WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a2-b1 | null | null | null | {'GAL2-FUC3': {'2': {'phi': -77.33, 'psi': 139.12, 'strain': 0.426, 'linkage': '1-2'}, '3': {'phi': -76.41, 'psi': 152.95, 'strain': 1.347, 'linkage': '1-2'}, '4': {'phi': -58.24, 'psi': 119.89, 'strain': 2.236, 'linkage': '1-2'}, '5': {'phi': -106.06, 'psi': 134.61, 'strain': 2.369, 'linkage': '1-2'}, '6': {'phi': -72... | {'GAL2-FUC3': {'2': {'phi': -77.33, 'psi': 139.12, 'strain': 0.426, 'linkage': '1-2'}, '3': {'phi': -76.4, 'psi': 152.96, 'strain': 1.347, 'linkage': '1-2'}, '4': {'phi': -58.37, 'psi': 120.04, 'strain': 1.886, 'linkage': '1-2'}, '5': {'phi': -106.08, 'psi': 134.62, 'strain': 2.369, 'linkage': '1-2'}, '6': {'phi': -72.... | {'GAL2-FUC3': {'2': {'phi': -77.33, 'psi': 139.12, 'strain': 0.426, 'linkage': '1-2'}, '3': {'phi': -76.41, 'psi': 152.95, 'strain': 1.347, 'linkage': '1-2'}, '4': {'phi': -58.24, 'psi': 119.89, 'strain': 2.236, 'linkage': '1-2'}, '5': {'phi': -106.06, 'psi': 134.61, 'strain': 2.369, 'linkage': '1-2'}, '6': {'phi': -72... | {'taxon_id': '10114', 'taxon_label': 'Rattus', 'evidence': [{'label': 'GlyTouCan(glycome-db)', 'id': 'glytoucan.org/Structures/Glycans/G67189MD'}]};{'taxon_id': '9606', 'taxon_label': 'Homo sapiens (human)', 'evidence': [{'label': 'GlyTouCan(glycome-db)', 'id': 'glytoucan.org/Structures/Glycans/G67189MD'}]};{'taxon_id'... | 2 | {'taxid': 9606, 'name': 'Homo sapiens', 'annotation_category': 'direct', 'evidence': [{'database': 'GlyCosmos', 'id': 'G67189MD', 'url': 'https://glycosmos.org/glycans/show/G67189MD'}], 'common_name': 'Human', 'glygen_name': 'Human', 'reference_species': 'Homo sapiens [9606]'};{'taxid': 9823, 'name': 'Sus scrofa', 'ann... | {'type': {'name': 'Other'}, 'subtype': {'name': 'Other'}} | null | {'id': '491859570', 'url': 'https://pubchem.ncbi.nlm.nih.gov/substance/491859570', 'database': 'PubChem Substance', 'categories': ['Chemical']};{'id': '643', 'database': 'Glycosciences.de', 'categories': ['Discontinued']};{'id': '10066', 'url': 'https://www.genome.jp/dbget-bin/www_bget?carbbank+10066', 'database': 'Car... | 424.23 | {'gnome_glygen_oglycans': 'no', 'sandbox': 'no', 'gnome_glygen': 'yes', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'no', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 984 | Saccharide | Hex(1)dHex(1) % 326.12129707 | freeEnd--?D-Gal--2a1L-Fuc,p$MONO,Und,0,0,freeEnd | null | {'related_accession': 'G04537GR', 'relationship': 'ancestor'};{'related_accession': 'G08012BR', 'relationship': 'ancestor'};{'related_accession': 'G08453HV', 'relationship': 'ancestor'};{'related_accession': 'G42494UJ', 'relationship': 'ancestor'};{'related_accession': 'G53862OE', 'relationship': 'ancestor'};{'related_... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 1.0.13'} |
./raw_dataGS00014/snfg.svg | ./torsion_data/GS00014_torsion_data.txt | {'Cluster 0': {'count': 13887, '4_2_phi_mean': -69.45, '4_2_psi_mean': 130.79, '3_2_phi_mean': -70.48, '3_2_psi_mean': -97.63, '4_2_phi_std': 8.26, '4_2_psi_std': 6.81, '3_2_phi_std': 9.73, '3_2_psi_std': 7.74}, 'Cluster 1': {'count': 9614, '4_2_phi_mean': -66.48, '4_2_psi_mean': 129.13, '3_2_phi_mean': -69.14, '3_2_ps... | G87205VF | GS00014 | DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAca1-OH | DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAc | Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc | α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)[α-L-Fucp-(1→3)]-D-GlcNAc | WURCS=2.0/4,4,3/[u2122h_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2 | RES,1b:b-dglc-HEX-1:5,2s:n-acetyl,3b:a-lgal-HEX-1:5|6:d,4b:b-dgal-HEX-1:5,5b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d,6s:n-acetyl,LIN,1:1d(2+1)2n,2:1o(3+1)3d,3:1o(4+1)4d,4:4o(3+2)5d,5:5d(5+1)6n, | O1C(O)[C@H](NC(C)=O)[C@@H](O[C@@H]2O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@]3(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C@H](O)[C@H](O)CO)O3)[C@H]2O)[C@H]1CO | null | 820.3 | {'motif': 'G30207PZ', 'motif_label': 'GM4'} | Fuc(a1-3);Neu5Ac(a2-3) | {'Neu5Ac': 1, 'Gal': 1, 'Fuc': 1, 'GlcNAc': 1} | {'Hex': 1, 'HexNAc': 1, 'Neu5Ac': 1, 'dHex': 1} | 14 | 15 | 23 | 10.856017 | {'Cluster 0': 34.71, 'Cluster 1': 24.03, 'Cluster 2': 21.65, 'Cluster 3': 16.36, 'Cluster 4': 3.24} | {'Cluster 0': 45.383, 'Cluster 1': 18.5031, 'Cluster 2': 15.2185, 'Cluster 3': 12.2813, 'Cluster 4': 2.4748, 'Cluster 5': 2.1973, 'Cluster 6': 1.3324, 'Cluster 7': 0.8074, 'Cluster 8': 0.5924, 'Cluster 9': 0.48, 'Cluster 10': 0.26, 'Cluster 11': 0.21, 'Cluster 12': 0.105, 'Cluster 13': 0.0675, 'Cluster 14': 0.065, 'Clu... | {'2': 0.3492940814952079, '3': 0.4246905800241308, '4': 0.42414413536420126, '5': 0.3262361058391968, '6': 0.3062112955530023, '7': 0.2624774236698168, '8': 0.260399948139211} | {'0': [1, 3, 10, 12, 14], '1': [5], '2': [0, 9], '3': [2, 4, 8], '4': [6, 7, 11, 13, 15]} | {'explained_variance_ratio': [0.14813452236287625, 0.11339584459059113, 0.08120681880476716, 0.04350134261370679, 0.038561878825415494, 0.03324458162813341, 0.0314877134669693, 0.0267991230577476, 0.024290732465027533, 0.02059740973126309], 'cumulative_variance': [0.14813452236287625, 0.2615303669534674, 0.342737185758... | 2 | GROMACS | GLYCAM_06j | 300 | 1 | 150 | DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAca1-OH | Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(a1- | α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)[α-L-Fucp-(1→3)]-α-D-GlcpNAc-(1→ | G07675NG | WURCS=2.0/4,4,3/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2 | DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAcb1-OH | Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1- | α-D-Neup5Ac-(2→3)-β-D-Galp-(1→4)[α-L-Fucp-(1→3)]-β-D-GlcpNAc-(1→ | G00054MO | WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2 | null | null | null | {'NDG2-FUC3': {'2': {'phi': -70.39, 'psi': -98.6, 'strain': -0.0, 'linkage': '1-3'}, '3': {'phi': -74.28, 'psi': -100.9, 'strain': 0.136, 'linkage': '1-3'}, '4': {'phi': -76.48, 'psi': -100.95, 'strain': 0.136, 'linkage': '1-3'}, '5': {'phi': -68.04, 'psi': -100.04, 'strain': 0.087, 'linkage': '1-3'}, '6': {'phi': -72.... | {'NDG2-FUC3': {'2': {'phi': -70.39, 'psi': -98.6, 'strain': -0.0, 'linkage': '1-3'}, '3': {'phi': -74.27, 'psi': -100.9, 'strain': 0.136, 'linkage': '1-3'}, '4': {'phi': -76.45, 'psi': -100.95, 'strain': 0.136, 'linkage': '1-3'}, '5': {'phi': -68.12, 'psi': -99.96, 'strain': 0.094, 'linkage': '1-3'}, '6': {'phi': -72.0... | {'NDG2-FUC3': {'2': {'phi': -70.39, 'psi': -98.6, 'strain': -0.0, 'linkage': '1-3'}, '3': {'phi': -74.28, 'psi': -100.9, 'strain': 0.136, 'linkage': '1-3'}, '4': {'phi': -76.48, 'psi': -100.95, 'strain': 0.136, 'linkage': '1-3'}, '5': {'phi': -68.04, 'psi': -100.04, 'strain': 0.087, 'linkage': '1-3'}, '6': {'phi': -72.... | {'taxon_id': '9606', 'taxon_label': 'Homo sapiens (human)', 'evidence': [{'label': 'GlyTouCan(glycome-db)', 'id': 'glytoucan.org/Structures/Glycans/G87205VF'}]} | 4 | {'taxid': 9031, 'name': 'Gallus gallus', 'annotation_category': 'subsumption', 'evidence': [{'database': 'Subsumption', 'id': 'G00054MO', 'url': 'https://www.glygen.org/glycan/G00054MO'}], 'common_name': 'Chicken', 'glygen_name': 'Chicken', 'reference_species': 'Gallus gallus [9031]'};{'taxid': 10029, 'name': 'Cricetul... | {'type': {'name': 'Other'}, 'subtype': {'name': 'Other'}} | null | {'id': '491920888', 'url': 'https://pubchem.ncbi.nlm.nih.gov/substance/491920888', 'database': 'PubChem Substance', 'categories': ['Chemical']};{'id': '2279', 'database': 'Glycosciences.de', 'categories': ['Discontinued']};{'id': '14199', 'url': 'https://www.genome.jp/dbget-bin/www_bget?carbbank+14199', 'database': 'Ca... | 1,030.53 | {'gnome_glygen_oglycans': 'no', 'sandbox': 'no', 'gnome_glygen': 'yes', 'gnome': 'yes', 'gnome_glycotree_oglycans': 'no', 'pdb': 'no', 'gnome_glygen_nglycans': 'no', 'gnome_glycotree_nglycans': 'no'} | 492 | Saccharide | HexNAc(1)Hex(1)dHex(1)NeuAc(1) % 820.29608631 | freeEnd--?D-GlcNAc(--3a1L-Fuc,p)--4b1D-Gal,p--3a2D-NeuAc,p$MONO,Und,0,0,freeEnd | {'id': 'GGM.000001', 'name': 'Type 2 LN', 'synonym': 'N-acetyllactosamine', 'keywords': 'LacNAc; N-acetyllactosamine; N-acetyllactosamine type 2'};{'id': 'GGM.000018', 'name': 'Lewis x', 'synonym': 'Le^x; Lex; SSEA-1', 'keywords': 'Lewis x'};{'id': 'GGM.000022', 'name': 'Sialyl Lewis x', 'synonym': 'SLe^x; SLex; Slex',... | {'related_accession': 'G01010HI', 'relationship': 'ancestor'};{'related_accession': 'G11499FP', 'relationship': 'ancestor'};{'related_accession': 'G13065CP', 'relationship': 'ancestor'};{'related_accession': 'G15602PX', 'relationship': 'ancestor'};{'related_accession': 'G15730NX', 'relationship': 'ancestor'};{'related_... | {'table_id': 'glycoprotein', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression', 'table_stats': [{'field': 'total', 'count': 0}, {'field': 'total_sites', 'count': 0}]};{'table_id': 'expression_tissue', 'table_stats': [{'field': 'total', 'count': 0}, {'field'... | {'type': 'added', 'description': 'introduced in data release 1.0.13'} |
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GlycoShape: A structural dataset of glycans
GlycoShape is a curated dataset of carbohydrate conformational ensembles derived from molecular dynamics simulations and structural analysis. The dataset aims to provide standardized structural representations of glycans and glycosidic torsions to support computational glycobiology, structural bioinformatics, and machine learning applications.
The dataset provides torsional information, conformational clusters, and representative structures for glycan fragments. It is designed to facilitate research on glycan conformational landscapes, glycosidic linkage preferences, and carbohydrate–protein recognition.
Dataset Description
A gift to Rosetta Commons.
Carbohydrates exhibit complex conformational behavior due to the flexibility of glycosidic bonds. Understanding these conformations is essential for studying:
glycan recognition by proteins
carbohydrate-binding specificity
glycan structural motifs
glyco-bioinformatics and machine learning models
GlycoShape (source: glycoshape.org) provides curated conformational ensembles with standardized torsion angle annotations and clustering results. The dataset contains glycosidic torsion trajectories and cluster assignments extracted from MD simulations and processed into easily usable tabular formats.
Dataset Reproduction
Primary clustered structures were downloaded in :
https://glycoshape.org/downloads
Secondary clustered structures were downloaded via :
$ python ./src/secondary_cluster_fetch.py
Torsion tables of secondary clustered structure were fetched via :
$ python ./src/fetch_torsion.py
The metadata table was generated via:
$ python ./src/data_extract.py
Dataset Fields
The MD structural files after primary clustering is in ./raw_data
The MD structural files after seconday clustering is in ./clustered_data.zip
The metadata is in glycoshape_data.csv includes:
| Field | Description |
|---|---|
| 'SNFG' | figure of Symbol Nomenclature for Glycans (SNFG) |
| 'torsion_table' | raw table of glycosidic bond torsions of glycan from MD simulation |
| 'torsion_analysis' | analysis of glycosidic bond torsions of glycan from MD simulation |
| 'glytoucan' | glytoucan ID |
| 'ID' | GlycoShape ID |
| 'name' | glycan name |
| 'glycam' | name in GLYCAM format |
| 'iupac' | name in IUPAC format |
| 'iupac_extended' | name in extended IUPAC format |
| 'wurcs' | name in extended WURCS |
| 'glycoct' | name in GLYCOCT |
| 'smiles' | SMILES format |
| 'oxford' | name in Oxford glycan notation system |
| 'mass' | molecular mass |
| 'motifs' | involving glycan motifs |
| 'termini' | termini monosaccharide unit |
| 'components' | monosaccharide components |
| 'composition' | monosaccharide composition |
| 'rot_bonds' | Number of Rotatable Bonds |
| 'hbond_donor' | Number of Hydrogen Bond Donors |
| 'hbond_acceptor' | Number of Hydrogen Bond Acceptors |
| 'entropy' | conformational entropy quantifies the degree of structural flexibility of the glycan, It measures how widely distributed the conformational ensemble is across clusters. |
| 'clusters' | the percentage of simulation frames that fall into seondary 5 conformational clusters |
| 'coverage_clusters' | the percentage of simulation frames that fall into primary conformational clusters according to torsions |
| 'silhouette_scores' | average silhouette score obtained for different numbers of clusters (k) during the secondary clustering |
| 'coverage_clusters_per_main' | a hierarchical grouping of the primary conformational clusters into 5 secondary cluster |
| 'pca_variance' | information of PCA analysis according to torsions |
| 'length' | MD simulation Length (μs) |
| 'package' | MD Engine |
| 'forcefield' | MD Force Field |
| 'temperature' | MD Temperature (K) |
| 'pressure' | MD Pressure (bar) |
| 'salt' | MD Salt (mM) |
| 'a_glycam' | GLYCAM ID of alpha anomer |
| 'a_iupac' | IUPAC of alpha anomer |
| 'a_iupac_extended' | extended IUPAC of alpha anomer |
| 'a_glytoucan' | Glytocan ID of beta anomer |
| 'a_wurcs' | WURCS iD of beta anomer |
| 'b_glycam' | GLYCAM ID of beta anomer |
| 'b_iupac' | IUPAC of beta anomer |
| 'b_iupac_extended' | extended IUPAC of beta anomer |
| 'b_glytoucan' | Glytocan ID of beta anomer |
| 'b_wurcs' | WURCS iD of beta anomer |
| 'common_names' | common name |
| 'description' | description |
| 'keywords' | keywords |
| 'calculated_torsion' | torsion information of archetype calculated from secondary clustered structure |
| 'a_calculated_torsion' | torsion information of alpha anomer calculated from secondary clustered structure |
| 'b_calculated_torsion' | torsion information of beta anomer calculated from secondary clustered structure |
| 'glycosmos' | organismal annotations from GlyCosmos |
| 'number_monosaccharides' | monosaccharide count |
| 'species' | organismal annotations from glygen |
| 'classification' | classifications |
| 'enzyme' | related enzyme |
| 'crossref' | reference |
| 'mass_pme' | Permethylated Mass |
| 'tool_support' | supporting tool |
| 'missing_score' | degree of missing structural information or incomplete sampling in the conformational dataset |
| 'glycan_type' | type of glycan |
| 'byonic' | glycan composition and theoretical mass used in glycoproteomics mass-spectrometry |
| 'gwb' | GlycoWorkbench format. |
| 'motifs' | glycan motif in GlycoMotif (GGM) database |
| 'subsumption' | subsumption relationships of this glycan within the GlyTouCan / GNOME glycan ontology hierarchy. |
| 'section_stats' | biological annotations |
| 'history' | version history in glycoshape |
Citation
Ives, C.M., Singh, O. et al. Restoring protein glycosylation with GlycoShape. Nat Methods (2024).
Licensing
All of the data provided is freely available for use under Creative Commons Attribution 4.0 (CC BY 4.0 Deed) licence terms
Dataset Card Authors
Yijie (Jacky) Luo : jacky233@163.com;
Ming Shen : mingshen01@gmail.com;
Kaley Chinoy : chinoykaley@gmail.com.
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