protein-ligand-interactions 开源项目推荐（113 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。

hkmztrk /DeepDTA

Source code for "DeepDTA: deep drug-target binding affinity prediction"

baker-laboratory /PLACER

PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

zaixizhang /PocketGen

PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets

huankoh /PSICHIC

PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data

pritampanda15 /PandaMap

Ligand-Protein Interaction Mapping

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]

zaixizhang /FLAG

Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs"

XieResearchGroup /Physics-aware-Multiplex-GNN

Source code for "A universal framework for accurate and efficient geometric deep learning of molecular systems" (Nature Scientific Reports)

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。

DrugBud-Suite /CADD_Vault

该项目在 GitHub 上没有填写描述

DrugBud-Suite /DockM8

All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.

sbl-sdsc /mmtf-pyspark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

sbl-sdsc /mmtf-workshop-2018

Structural Bioinformatics Training Workshop & Hackathon 2018

lucidrains /neural-plexer-pytorch

Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, in Pytorch

dwhswenson /contact_map

Contact map analysis for biomolecules; based on MDTraj

chengwang88 /deltavina

DeltaVina scoring function

lhm30 /PIDGINv3

Protein target prediction using random forests and reliability-density neighbourhood analysis

ZhaohanM /FusionDTI

[EMNLP 2025]* FusionDTI utilises a Token-level Fusion module to effectively learn fine-grained information for Drug-Target Interaction Prediction.

YangLing0818 /IRDiff

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