Daily Papers

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein binding pocket, neglecting the intrinsic flexibility of proteins and the conformational rearrangements induced by ligand binding, limiting their applicability in practical drug discovery. Here, we propose Apo2Mol, a diffusion-based generative framework for 3D molecule design that explicitly accounts for conformational flexibility in protein binding pockets. To support this, we curate a dataset of over 24,000 experimentally resolved apo-holo structure pairs from the Protein Data Bank, enabling the characterization of protein structure changes associated with ligand binding. Apo2Mol employs a full-atom hierarchical graph-based diffusion model that simultaneously generates 3D ligand molecules and their corresponding holo pocket conformations from input apo states. Empirical studies demonstrate that Apo2Mol can achieve state-of-the-art performance in generating high-affinity ligands and accurately capture realistic protein pocket conformational changes.

Multimodal Large Language Models (MLLMs) are powerful at integrating diverse data, but they often struggle with complex reasoning. While Reinforcement learning (RL) can boost reasoning in LLMs, applying it to MLLMs is tricky. Common issues include a drop in performance on general tasks and the generation of overly detailed or "overthinking" reasoning. Our work investigates how the KL penalty and overthinking affect RL training in MLLMs. We propose Asymmetric Policy Optimization (APO) to address these issues, which divides the sampled responses into positive and negative groups. For positive samples, Difficulty-Adaptive Divergence Shaping (DADS) is introduced to dynamically adjust the KL divergence weight based on their difficulty. This method prevents policy entropy from dropping sharply, improves training stability, utilizes samples better, and preserves the model's existing knowledge. For negative samples, Suboptimal Trajectory Complexity Regularization (STCR) is proposed to penalize overly long responses. This helps mitigate overthinking and encourages more concise reasoning while preserving the model's explorative capacity. We apply our method to Qwen2.5-VL-3B, creating View-R1-3B. View-R1-3B significantly enhances reasoning capabilities, showing an average 7\% gain over the base model and outperforming larger MLLMs (7-11B) on various reasoning benchmarks. Importantly, unlike other reasoning-tuned MLLMs that often degrade on general tasks, View-R1-3B maintains consistent improvement, demonstrating superior generalization. These results highlight the effectiveness and broad applicability of our DADS and STCR techniques for advancing complex multimodal reasoning in MLLMs. The code will be made available at https://github.com/Indolent-Kawhi/View-R1.

The basic question-answering format of large language models involves inputting a prompt and receiving a response, and the quality of the prompt directly impacts the effectiveness of the response. Automated Prompt Optimization (APO) aims to break free from the cognitive biases of manually designed prompts and explores a broader design space for prompts. However, existing APO methods suffer from limited flexibility of fixed templates and inefficient search in prompt spaces as key issues. To this end, we propose a Multi-Agent framework Incorporating Socratic guidance (MARS), which utilizes multi-agent fusion technology for automatic planning, with gradual continuous optimization and evaluation. Specifically, MARS comprises seven agents, each with distinct functionalities, which autonomously use the Planner to devise an optimization path that ensures flexibility. Additionally, it employs a Teacher-Critic-Student Socratic dialogue pattern to iteratively optimize the prompts while conducting effective search. We conduct extensive experiments on various datasets to validate the effectiveness of our method, and perform additional analytical experiments to assess the model's advancement as well as the interpretability.

Prompting is fundamental to unlocking the full potential of large language models. To automate and enhance this process, automatic prompt optimization (APO) has been developed, demonstrating effectiveness primarily in text-only input scenarios. However, extending existing APO methods to multimodal tasks, such as video-language generation introduces two core challenges: (i) visual token inflation, where long visual token sequences restrict context capacity and result in insufficient feedback signals; (ii) a lack of process-level supervision, as existing methods focus on outcome-level supervision and overlook intermediate supervision, limiting prompt optimization. We present UniAPO: Unified Multimodal Automated Prompt Optimization, the first framework tailored for multimodal APO. UniAPO adopts an EM-inspired optimization process that decouples feedback modeling and prompt refinement, making the optimization more stable and goal-driven. To further address the aforementioned challenges, we introduce a short-long term memory mechanism: historical feedback mitigates context limitations, while historical prompts provide directional guidance for effective prompt optimization. UniAPO achieves consistent gains across text, image, and video benchmarks, establishing a unified framework for efficient and transferable prompt optimization.