Awesome-Molecular-Docking

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

We will update this repository regularly. :sunglasses:

If you want to add related works to this repository, please feel free to contact me via [email protected].

Welcome to contribute to this repository! :clap:

Related Survey

• 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. [Paper]

Dataset

• PDBBind
• Structural Antibody Database (SAbDab)
• Database of Interacting Protein Structures (DIPS)

Software for Docking

• ATTRACT
• HDOCK
• CLUSPRO
• PATCHDOCK

Molecule-Protein Docking

• Corso, Gabriele, et al. "DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking." arXiv preprint arXiv:2210.01776 (2022). [Paper][Code]
• 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][Code]
• Stärk, Hannes, et al. "Equibind: Geometric deep learning for drug binding structure prediction." International Conference on Machine Learning. PMLR, 2022. [Paper][Code]

Protein-Protein Docking

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

Antibody Design

• 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][Code]
• Jin, Wengong, Regina Barzilay, and Tommi Jaakkola. "Antibody-antigen docking and design via hierarchical structure refinement." International Conference on Machine Learning. PMLR, 2022. [Paper][Code]

Molecular Dynamics Simulation

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

Binding Site Identification

• 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. [Paper][Code]

See Also

• awesome-python-chemistry
• awesome-cheminformatics
• deeplearning-biology
• awesome-small-molecule-ml
• Survey_AI_Drug_Discovery