Molecular Docking Tools
Gnina 1.0
Date: 9-Jun-21
Paper: GNINA 1.0: Molecular docking with deep learning
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1186/s13321-021-00522-2
Code: https://github.com/gnina/gnina
EquiBind
Date: 7-Feb-22
Paper: EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction
Task: Docking (unreliable)
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.48550/arXiv.2202.05146
Code: https://github.com/HannesStark/EquiBind
DiffDock
Date: 4-Oct-22
Paper: DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Limited
DOI: https://doi.org/10.48550/arXiv.2210.01776
Code: https://github.com/gcorso/DiffDock
TankBind
Date: 25-Oct-22
Paper: TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction
Task: Docking (unreliable)
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1101/2022.06.06.495043
Code: https://github.com/luwei0917/TankBind
EDM-Dock
Date: 14-Mar-23
Paper: Deep Learning Model for Efficient Protein?Ligand Docking with Implicit Side-Chain Flexibility
Task: Flexible docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1021/acs.jcim.2c01436
Code: https://github.com/MatthewMasters/EDM-Dock
DiffDock-PP
Date: 8-Apr-23
Paper: DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models
Task: Protein-protein docking
Receptor: Protein
Ligand: Protein
VS support: Unknown
DOI: https://doi.org/10.48550/arXiv.2304.03889
Code: https://github.com/ketatam/DiffDock-PP
KarmaDock
Date: 21-Sep-23
Paper: Efficient and accurate large library ligand docking with KarmaDock
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1038/s43588-023-00511-5
Code: https://github.com/schrojunzhang/KarmaDock
GAABind
Date: 14-Dec-23
Paper: GAABind: a geometry-aware attention-based network for accurate protein?ligand binding pose and binding affinity prediction
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: No
DOI: https://doi.org/10.1093/bib/bbad462
Code: https://github.com/Mercuryhs/GAABind
CarsiDock
Date: 19-Dec-23
Paper: CarsiDock: a deep learning paradigm for accurate protein?ligand docking and screening based on large-scale pre-training
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1039/D3SC05552C
Code: https://github.com/carbonsilicon-ai/CarsiDock
DynamicBind
Date: 5-Feb-24
Paper: DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
Task: Docking with flexible C-alpha
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1038/s41467-024-45461-2
Code: https://github.com/luwei0917/DynamicBind
DiffBindFR
Date: 9-Apr-24
Paper: DiffBindFR: an SE(3) equivariant network for flexible protein?ligand docking
Task: Flexible docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1039/D3SC06803J
Code: https://github.com/HBioquant/DiffBindFR
Uni-Mol Docking 2
Date: 20-May-24
Paper: Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.48550/arXiv.2405.11769
Code: https://github.com/deepmodeling/Uni-Mol/tree/main/unimol_docking_v2
FABind+
Date: 29-May-24
Paper: FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.48550/arXiv.2403.20261
Code: https://github.com/QizhiPei/FABind
GalaxyDock-DL
Date: 7-Aug-24
Paper: GalaxyDock-DL: Protein?Ligand Docking by Global Optimization and Neural Network Energy
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1021/acs.jctc.4c00385
Code: https://github.com/seoklab/galaxydock_dl
DeltaDock
Date: 15-Oct-24
Paper: DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.48550/arXiv.2410.11224
Code: https://github.com/jiaxianyan/DeltaDock
OpenDock
Date: 21-Oct-24
Paper: OpenDock: a pytorch-based open-source framework for protein?ligand docking and modelling
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1093/bioinformatics/btae628
Code: https://github.com/guyuehuo/opendock
ApoDock
Date: 25-Nov-24
Paper: ApoDock: Ligand-Conditioned Sidechain Packing for Flexible Molecular Docking
Task: Flexible docking
Receptor: Protein
Ligand: Small molecules
VS support: No
DOI: https://doi.org/10.1101/2024.11.22.624942
Code: https://github.com/DingLuoXMU/ApoDock_public
Interformer
Date: 25-Nov-24
Paper: Interformer: an interaction-aware model for protein-ligand docking and affinity prediction
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1038/s41467-024-54440-6
Code: https://github.com/tencent-ailab/Interformer
SurfDock
Date: 27-Nov-24
Paper: SurfDock is a surface-informed diffusion generative model for reliable and accurate protein?ligand complex prediction
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1038/s41592-024-02516-y
Code: https://github.com/CAODH/SurfDock
PPDock
Date: 15-Jan-25
Paper: PPDock: Pocket Prediction-Based Protein?Ligand Blind Docking
Task: Docking via Dock
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1021/acs.jcim.4c01373
Code: https://github.com/JieDuTQS/PPDock
DENOISer
Date: 10-Feb-25
Paper: Physics-Inspired Accuracy Estimator for Model-Docked Ligand Complexes
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1021/acs.jctc.4c01373
Code: https://github.com/HParklab/DENOISer
GerNA-Bind
Date: 19-Feb-25
Paper: GerNA-Bind: Geometric-enhanced RNA-ligand Binding Specificity Prediction with Deep Learning
Task: Docking
Receptor: RNA
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1101/2025.02.15.638393
Code: https://github.com/GENTEL-lab/GerNA-Bind
Gnina 1.3
Date: 2-Mar-25
Paper: GNINA 1.3: the next increment in molecular docking with deep learning
Task: Docking (inc. covalent)
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1186/s13321-025-00973-x
Code: https://github.com/gnina/gnina
FeatureDock
Date: 4-Mar-25
Paper: FeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Unknown
DOI: https://doi.org/10.1038/s44386-025-00005-6
Code: https://github.com/xuhuihuang/featuredock
PhysDock
Date: 3-May-25
Paper: PhysDock: A Physics-Guided All-Atom Diffusion Model for Protein-Ligand Complex Prediction
Task: Docking
Receptor: Protein
Ligand: Small molecules
VS support: Yes
DOI: https://doi.org/10.1101/2025.04.28.650887
Code: https://github.com/KexinZhangResearch/PhysDock