protein-ligand-docking

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

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

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning. Official Implementation of PocketVina

[ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation

GaudiMM: A modular optimization platform for molecular design

Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.

Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"

A novel approach to pose selection in protein-ligand docking based on graph theory.

Flexible Artificial Intelligence Docking

A python script for PyMol to make protein-ligand interaction images.

DOCK6 is a molecular docking program.

LigTMap currently supports prediction for 17 protein target classes that include 6000+ protein targets.

UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

Preprocessing file generator (v1) and hosted Boltz-2 API builder/submitter (v2.0): binary, ternary, or N-body protein-ligand-DNA-RNA binding prediction.

Root-mean-square deviation of atomic positions

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes

NRGsuite is a PyMOL plugin (GUI) for FlexAID

PIAWeb - a graphical web interface for PIA