protein-ligand-docking 开源项目推荐（41 个）

rdk /p2rank

P2Rank：基于机器学习从蛋白质结构预测蛋白-配体结合位点。

Thinklab-SJTU /awesome-molecular-docking

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

rxdock /rxdock

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]

BIMSBbioinfo /PocketVina

PocketVina 的官方实现：GPU 加速的蛋白质-配体对接，对接至 P2Rank 找到的口袋，并支持多口袋条件。

YangLing0818 /IRDiff

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

insilichem /gaudi

GaudiMM：用于分子设计的模块化优化平台

LDeng0205 /confidence-bootstrapping

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

suneelbvs /DiffDock

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

docking-org /dock6

DOCK6 is a molecular docking program.

rasbt /siteinterlock

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

NRGlab /FlexAID

Flexible Artificial Intelligence Docking

quantaosun /Pymol_Script

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

ShirleyWISiu /LigTMap

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

LigandPro /Bento

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

Ayushmania2002 /boltzyml

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

neudinger /pyDockRMSD

Root-mean-square deviation of atomic positions

psa-lab /siteinterlock

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

rasbt /protein-recognition-index

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

NRGlab /NRGsuite

NRGsuite is a PyMOL plugin (GUI) for FlexAID

michabirklbauer /PIAWeb

PIAWeb - a graphical web interface for PIA