structural-biology

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a-r-j /graphein

Sponsor

Star1.1k

Protein Graph Library

python bioinformatics deep-learning structural-biology protein-data-bank protein-structure computational-biology pytorch protein drug-discovery rna interactome protein-design interactomics geometric-deep-learning ppi-networks graph-neural-networks pytorch-geometric gene-regulatory-networks dgl

UpdatedMar 3, 2025
Jupyter Notebook

BradyAJohnston /MolecularNodes

Star987

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

blender proteins structural-biology pdb protein-data-bank protein-structure visualisation molecule molecular-dynamics molecular-graphics protein biochemistry molecular blender-addon molecular-modeling sciart protein-visualization geometry-nodes

UpdatedMar 17, 2025
Python

biotite-dev /biotite

Star762

A comprehensive library for computational molecular biology

bioinformatics structural-biology computational-biology pdb-files sequence-analysis

UpdatedMar 16, 2025
Python

haddocking /pdb-tools

Star399

A dependency-free cross-platform swiss army knife for PDB files.

python bioinformatics structural-biology pdb protein structural-bioinformatics utrecht-university rcsb

UpdatedSep 3, 2024
Python

jonathanking /sidechainnet

Star349

An all-atom protein structure dataset for machine learning.

machine-learning deep-learning structural-biology protein-structure dataset

UpdatedMar 16, 2024
Python

lightdock /lightdock

Star324

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

bioinformatics chemistry structural-biology molecular-structures protein-structure artificial-intelligence dna protein proteomics docking peptides molecular-biology protein-design protein-protein-interaction swarm-intelligence structural-bioinformatics protein-dna-interactions bioinformatics-tool glowworm-swarm-optimization protein-docking

UpdatedDec 12, 2024
Python

project-gemmi /gemmi

Star250

macromolecular crystallography library and utilities

structural-biology molecular-structures protein-structure crystallography cif ccp4 mmcif pdb-files mtz

UpdatedMar 17, 2025
C++

drorlab /pensa

Star136

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

structural-biology molecular-dynamics biophysics biomolecules

UpdatedFeb 12, 2025
Python

mittinatten /freesasa

Star128

C-library for calculating Solvent Accessible Surface Areas

c bioinformatics structural-biology pdb

UpdatedMay 27, 2024
C

Genentech /equifold

Star120

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

machine-learning proteins structural-biology structure-prediction

UpdatedJan 8, 2023
Python

phonchi /Computational-CryoEM

Star116

A curated list of awesome computational cryo-EM methods.

structural-biology computational-biology electron-microscopy cryo-em single-particle-analisys cryoem

UpdatedMar 2, 2025
Jupyter Notebook

jonathanking /protein-transformer

Star111

Predicting protein structure through sequence modeling

machine-learning structural-biology protein-structure computational-biology attention sequence-to-sequence

UpdatedMay 4, 2020
Jupyter Notebook

SBRG /ssbio

Star107

A Python framework for structural systems biology

structural-biology protein-structure systems-biology cobrapy constraint-based-modeling structural-systems-biology

UpdatedDec 7, 2020
Python

samirelanduk /atomium

Sponsor

Star105

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

chemistry biology proteins structural-biology molecules

UpdatedDec 7, 2023
Python

molstar /VSCoding-Sequence

Star103

VSCode Extension for interactively visualising protein structure data in the editor

structural-biology pdb protein-structure structure vscode molecule protein vscode-extension pdb-files molstar

UpdatedNov 28, 2024
TypeScript

BioJulia /BioStructures.jl

Star99

A Julia package to read, write and manipulate macromolecular structures

bioinformatics biology structural-biology pdb julia protein-structure structural-bioinformatics biojulia

UpdatedMar 17, 2025
Julia

lbcb-sci /RiNALMo

Star89

RiboNucleic Acid (RNA) Language Model

bioinformatics rna-seq biology structural-biology rna language-model secondary-structure rna-structure-prediction rna-secondary-structure foundation-model splice-site-prediction

UpdatedMar 17, 2025
Python

cbalbin-bio /pymol-color-alphafold

Star87

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

bioinformatics structural-biology pymol-plugin protein-structure computational-biology pymol alphafold alphafold2

UpdatedJul 23, 2024
Python

I2PC /scipion

Star80

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)

python c-plus-plus workflow structural-biology image-processing reproducible-science usability electron-microscopy cryo-em single-particle-analisys

UpdatedApr 26, 2023
Python

salilab /imp

Star76

The Integrative Modeling Platform

python c-plus-plus structural-biology protein-structure integrative-modeling

UpdatedMar 7, 2025
C++

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