However, these methods have notable limitations.

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However, these methods have notable limitations.

Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-efficient, search-based docking framework that combines pocket prediction with systematic multi-pocket exploration. We evaluate PocketVina across four established benchmarks--PDBbind2020 (timesplit and unseen), DockGen, Astex, and PoseBusters--and observe consistently strong performance in sampling physically valid docking poses. PocketVina achieves state-of-the-art performance when jointly considering ligand RMSD and physical validity (PB-valid), while remaining competitive with deep learning-based approaches in terms of RMSD alone, particularly on structurally diverse and previously unseen targets. PocketVina also maintains state-of-the-art physically valid docking accuracy across ligands with varying degrees of flexibility. We further introduce TargetDock-AI, a benchmarking dataset we curated, consisting of over 500000 protein-ligand pairs, and a partition of the dataset labeled with PubChem activity annotations. On this large-scale dataset, PocketVina successfully discriminates active from inactive targets, outperforming a deep learning baseline while requiring significantly less GPU memory and runtime. PocketVina offers a robust and scalable docking strategy that requires no task-specific training and runs efficiently on standard GPUs, making it well-suited for high-throughput virtual screening and structure-based drug discovery.

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding to the same target protein tend to adopt similar poses, we propose \textsc{GroupBind}, a novel molecular docking framework that simultaneously considers multiple ligands docking to a protein. This is achieved by introducing an interaction layer for the group of ligands and a triangle attention module for embedding protein-ligand and group-ligand pairs. By integrating our approach with diffusion-based docking model, we set a new S performance on the PDBBind blind docking benchmark, demonstrating the effectiveness of our proposed molecular docking paradigm.

The diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, with DiffDock showing superior performance. Here, we employ a fully automatic workflow using the Surflex-Dock methods to generate a fair baseline for conventional docking approaches. Results were generated for the common and expected situation where a binding site location is known and also for the condition of an unknown binding site. For the known binding site condition, Surflex-Dock success rates at 2.0 Angstroms RMSD far exceeded those for DiffDock (Top-1/Top-5 success rates, respectively, were 68/81% compared with 45/51%). Glide performed with similar success rates (67/73%) to Surflex-Dock for the known binding site condition, and results for AutoDock Vina and Gnina followed this pattern. For the unknown binding site condition, using an automated method to identify multiple binding pockets, Surflex-Dock success rates again exceeded those of DiffDock, but by a somewhat lesser margin. DiffDock made use of roughly 17,000 co-crystal structures for learning (98% of PDBBind version 2020, pre-2019 structures) for a training set in order to predict on 363 test cases (2% of PDBBind 2020) from 2019 forward. DiffDock's performance was inextricably linked with the presence of near-neighbor cases of close to identical protein-ligand complexes in the training set for over half of the test set cases. DiffDock exhibited a 40 percentage point difference on near-neighbor cases (two-thirds of all test cases) compared with cases with no near-neighbor training case. DiffDock has apparently encoded a type of table-lookup during its learning process, rendering meaningful applications beyond its reach. Further, it does not perform even close to competitively with a competently run modern docking workflow.

Molecular docking is a major element in drug discovery and design. It enables the prediction of ligand-protein interactions by simulating the binding of small molecules to proteins. Despite the availability of numerous docking algorithms, there is no single algorithm consistently outperforms the others across a diverse set of docking scenarios. This paper introduces GNNAS-Dock, a novel Graph Neural Network (GNN)-based automated algorithm selection system for molecular docking in blind docking situations. GNNs are accommodated to process the complex structural data of both ligands and proteins. They benefit from the inherent graphlike properties to predict the performance of various docking algorithms under different conditions. The present study pursues two main objectives: 1) predict the performance of each candidate docking algorithm, in terms of Root Mean Square Deviation (RMSD), thereby identifying the most accurate method for specific scenarios; and 2) choose the best computationally efficient docking algorithm for each docking case, aiming to reduce the time required for docking while maintaining high accuracy. We validate our approach on PDBBind 2020 refined set, which contains about 5,300 pairs of protein-ligand complexes. Our strategy is performed across a portfolio of 6 different state-of-the-art docking algorithms.

While there has been discussion about noise levels in molecular docking datasets such as PDBBind, a thorough analysis of their physical/chemical and bioactivity noise characteristics is still lacking. PoseCheck addresses this issue by examining molecular strain energy, molecular-protein clashes, and interactions, but it is primarily created for $de$ $novo$ drug design. Another important metric in molecular docking, Binding Affinity Energy, is better assessed by the new empirical score function, AA-Score, which has demonstrated improved performance over existing methods. To tackle these challenges, we propose the COMPASS method, which integrates the PoseCheck and AA-Score modules. This approach evaluates dataset noise levels and the physical/chemical and bioactivity feasibility of docked molecules. Our analysis of the PDBBind dataset using COMPASS reveals significant noise in the ground truth data. Additionally, we incorporate COMPASS with the state-of-the-art molecular docking method, DiffDock, in inference mode to achieve efficient and accurate assessments of docked ligands. Finally, we propose a new paradigm to enhance model performance for molecular docking through fine-tuning and discuss the potential benefits of this approach. The source code is available publicly at https://github.com/BIMSBbioinfo/Compass.

This work introduces GeoDirDock (GDD), a novel approach to molecular docking that enhances the accuracy and physical plausibility of ligand docking predictions. GDD guides the denoising process of a diffusion model along geodesic paths within multiple spaces representing translational, rotational, and torsional degrees of freedom. Our method leverages expert knowledge to direct the generative modeling process, specifically targeting desired protein-ligand interaction regions. We demonstrate that GDD significantly outperforms existing blind docking methods in terms of RMSD accuracy and physicochemical pose realism. Our results indicate that incorporating domain expertise into the diffusion process leads to more biologically relevant docking predictions. Additionally, we explore the potential of GDD for lead optimization in drug discovery through angle transfer in maximal common substructure (MCS) docking, showcasing its capability to predict ligand orientations for chemically similar compounds accurately.

Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are often slow and costly. The advent of deep learning-based approaches has shown significant promise, offering increases in both accuracy and efficiency. Building upon the foundational work of FABind, a model designed with a focus on speed and accuracy, we present FABind+, an enhanced iteration that largely boosts the performance of its predecessor. We identify pocket prediction as a critical bottleneck in molecular docking and propose a novel methodology that significantly refines pocket prediction, thereby streamlining the docking process. Furthermore, we introduce modifications to the docking module to enhance its pose generation capabilities. In an effort to bridge the gap with conventional sampling/generative methods, we incorporate a simple yet effective sampling technique coupled with a confidence model, requiring only minor adjustments to the regression framework of FABind. Experimental results and analysis reveal that FABind+ remarkably outperforms the original FABind, achieves competitive state-of-the-art performance, and delivers insightful modeling strategies. This demonstrates FABind+ represents a substantial step forward in molecular docking and drug discovery. Our code is in https://github.com/QizhiPei/FABind.