awesome-molecular-docking

Bioinformatics toolkit

Curated list of resources and tools for molecular docking and related tasks in bioinformatics.

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

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ai-aided-drug-discoveryawesomeawesome-listbindingbioinformaticsdeep-learningdrug-designdrug-discoverydrug-protein-interactionsdrugaiequivariant-representationsgenerative-modelgeometric-deep-learningmachine-learningmolecular-dockingmolecular-dynamicsoptimal-transportpaper-listprotein-ligand-dockingprotein-protein-interaction

Paper Crampon, Kevin, et al. "Machine-learning methods for ligand–protein molecular docking." Drug discovery today (2021). [ ]
Paper Harmalkar, Ameya, and Jeffrey J. Gray. "Advances to tackle backbone flexibility in protein docking." Current opinion in structural biology 67 (2021): 178-186. [ ]

Awesome-Molecular-Docking / Molecule-Protein Docking
Paper Corso, Gabriele, et al. "DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking." arXiv preprint arXiv:2210.01776 (2022). [ ][ ]
Paper Zhang, Yangtian, et al. "E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking." arXiv preprint arXiv:2210.06069 (2022). [ ]
Paper Lu, Wei, et al. "TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction." Advances in Neural Information Processing Systems. 2022.[ ][ ]
Paper Stärk, Hannes, et al. "Equibind: Geometric deep learning for drug binding structure prediction." International Conference on Machine Learning. PMLR, 2022. [ ][ ]

Awesome-Molecular-Docking / Protein-Protein Docking
Paper Ganea, Octavian-Eugen, et al. "Independent se (3)-equivariant models for end-to-end rigid protein docking." International Conference on Learning Representations (2022). [ ][ ]

Awesome-Molecular-Docking / Antibody Design
Paper Luo, S., Su, Y., Peng, X., Wang, S., Peng, J., & Ma, J. Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. In Advances in Neural Information Processing Systems. [ ][ ]
Paper Jin, Wengong, Regina Barzilay, and Tommi Jaakkola. "Antibody-antigen docking and design via hierarchical structure refinement." International Conference on Machine Learning. PMLR, 2022. [ ][ ]

Awesome-Molecular-Docking / Molecular Dynamics Simulation
Paper Fu, Xiang, et al. "Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning." arXiv preprint arXiv:2204.10348 (2022). [ ][ ]

Awesome-Molecular-Docking / Binding Site Identification
Paper Freyr, et al. "Fast end-to-end learning on protein surfaces." Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. 2021. [ ]
Paper Gainza, Pablo, et al. "Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning." Nature Methods 17.2 (2020): 184-192. [ ][ ]

Awesome-Molecular-Docking / See Also
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awesome-cheminformatics 703 9 months ago
deeplearning-biology 2,022 4 months ago
awesome-small-molecule-ml 201 about 1 year ago
Survey_AI_Drug_Discovery 315 8 months ago

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