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awesome-molecular-docking

by Thinklab-SJTU

awesome listpushed over 3 years ago

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

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Bioinformatics toolkit

A curated list of resources and tools for molecular docking and related tasks in bioinformatics

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What's in the list

17 links in 7 sections, with live GitHub stats.activeno commit in 2y

  • 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. [ ]

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. [ ][ ]

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