protein-docking 开源项目推荐（21 个）

PaddlePaddle /PaddleHelix

具备大规模表示学习和多任务深度学习的生物计算平台“螺旋桨”生物计算工具集

Graylab /DL4Proteins-notebooks

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

RosettaCommons /PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

lightdock /lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

ketatam /DiffDock-PP

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

haddocking /arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

rvhonorato /gdock

Mirror of https://codeberg.org/rvhonorato/gdock >> development happens on Codeberg

Shen-Lab /BAL

Bayesian Active Learning for Optimization and Uncertainty Quantification with Applications to Protein Docking

tuplexyz /PD-1_Fab_Diffusion

PD-1 Targeted Antibody Discovery Using AI Protein Diffusion

haddocking /haddock-restraints

Generate restraints to be used in HADDOCK

sabifo4 /VSpipe

VSpipe - A pipeline to carry out virtual screenings

thuxugang /opus_fold3

OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow

colbyford /SARS-CoV-2_BA.2.86_Spike-RBD_Predictions

Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 with In Silico Protein Modeling and Docking

zakimjz /ContextShapes

ContextShapes Algorithm for rigid-body protein shape matching and docking

JitheshMithra /BINDops

Fast generative peptide-protein docking without computing MSAs. SE(3) flow matching on a DiffPepDock trunk with an ESM2-conditioned zero-init adapter. 38.8% acceptable (oracle), 9.2% top-1 on 304 blind complexes. Includes training code, verification gates, and documentation

SidSin0809 /compile_hdock_excel

Scrapes HDOCK job result pages, extracts the “Summary of the Top 10 Models” tables for any number of complexes, and builds a single-sheet Excel workbook with embedded download links to each job’s full results archive.

dalalalhabad /PfMSP3.1-SPAM-Structural-Characterisation

Computational structural characterisation of PfMSP3.1 SPAM, including modelling, MD, docking, AlphaFold and experimental NMR-restraint reassessment.

Harishreem /huntingtons-disease-protein-modeling

Structural bioinformatics pipeline investigating Huntington's disease mechanisms by modeling and docking mutant HTT-HAP40 protein complexes.

pyDock /pyProCT

🔬 pyProCT (Python 3 fork) brings the original pyProCT clustering toolkit back to life under modern Python. ⚙️ This version fixes Python 2 legacy issues, updates Cython extensions, adapts to recent NumPy/SciPy APIs, and ensures all clustering algorithms and postprocessing actions work end-to-end.

ikshanbio /A-Protein-Docking-Workflow

A protein-ligand docking workflow based on rigid sidechain docking with Autodock Vina.