Molecular Docking Tools

Date Name Title Receptor Ligand VS support Code
9-Jun-21 Gnina 1.0 GNINA 1.0: Molecular docking with deep learning Protein Small molecules Yes Link
7-Feb-22 EquiBind EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Protein Small molecules Yes Link
4-Oct-22 DiffDock DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Protein Small molecules Limited Link
25-Oct-22 TankBind TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction Protein Small molecules Yes Link
14-Mar-23 EDM-Dock Deep Learning Model for Efficient Protein?Ligand Docking with Implicit Side-Chain Flexibility Protein Small molecules Yes Link
8-Apr-23 DiffDock-PP DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models Protein Protein Unknown Link
21-Sep-23 KarmaDock Efficient and accurate large library ligand docking with KarmaDock Protein Small molecules Yes Link
14-Dec-23 GAABind GAABind: a geometry-aware attention-based network for accurate protein?ligand binding pose and binding affinity prediction Protein Small molecules No Link
19-Dec-23 CarsiDock CarsiDock: a deep learning paradigm for accurate protein?ligand docking and screening based on large-scale pre-training Protein Small molecules Unknown Link
5-Feb-24 DynamicBind DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model Protein Small molecules Unknown Link
9-Apr-24 DiffBindFR DiffBindFR: an SE(3) equivariant network for flexible protein?ligand docking Protein Small molecules Unknown Link
20-May-24 Uni-Mol Docking 2 Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction Protein Small molecules Unknown Link
29-May-24 FABind+ FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation Protein Small molecules Yes Link
7-Aug-24 GalaxyDock-DL GalaxyDock-DL: Protein?Ligand Docking by Global Optimization and Neural Network Energy Protein Small molecules Unknown Link
15-Oct-24 DeltaDock DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking Protein Small molecules Yes Link
21-Oct-24 OpenDock OpenDock: a pytorch-based open-source framework for protein?ligand docking and modelling Protein Small molecules Unknown Link
25-Nov-24 ApoDock ApoDock: Ligand-Conditioned Sidechain Packing for Flexible Molecular Docking Protein Small molecules No Link
25-Nov-24 Interformer Interformer: an interaction-aware model for protein-ligand docking and affinity prediction Protein Small molecules Yes Link
27-Nov-24 SurfDock SurfDock is a surface-informed diffusion generative model for reliable and accurate protein?ligand complex prediction Protein Small molecules Yes Link
15-Jan-25 PPDock PPDock: Pocket Prediction-Based Protein?Ligand Blind Docking Protein Small molecules Unknown Link
10-Feb-25 DENOISer Physics-Inspired Accuracy Estimator for Model-Docked Ligand Complexes Protein Small molecules Unknown Link
19-Feb-25 GerNA-Bind GerNA-Bind: Geometric-enhanced RNA-ligand Binding Specificity Prediction with Deep Learning RNA Small molecules Unknown Link
2-Mar-25 Gnina 1.3 GNINA 1.3: the next increment in molecular docking with deep learning Protein Small molecules Yes Link
4-Mar-25 FeatureDock FeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer Protein Small molecules Unknown Link
3-May-25 PhysDock PhysDock: A Physics-Guided All-Atom Diffusion Model for Protein-Ligand Complex Prediction Protein Small molecules Yes Link

 VS support: Virtual screening support based on the running time reported in the original paper of the tool.