awesome-molecular-docking
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
AI summary
Bioinformatics toolkit
A curated list of resources and tools for molecular docking and related tasks in bioinformatics
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- entries
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- #ai-aided-drug-discovery
- #awesome
- #awesome-list
- #binding
- #bioinformatics
- #deep-learning
- #drug-design
- #drug-discovery
- #drug-protein-interactions
- #drugai
- #equivariant-representations
- #generative-model
- #geometric-deep-learning
- #machine-learning
- #molecular-docking
- #molecular-dynamics
- #optimal-transport
- #paper-list
- #protein-ligand-docking
- #protein-protein-interaction
What's in the list
17 links in 7 sections, with live GitHub stats.activeno commit in 2y
Related Survey
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. [ ][ ]
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). [ ][ ]
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. [ ][ ]
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). [ ][ ]
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. [ ][ ]
See Also
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