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biopython /biopython

Official git repository for Biopython (originally converted from CVS)

python bioinformatics genomics protein-structure dna protein biopython phylogenetics sequence-alignment

UpdatedOct 31, 2025
Python

graphein

a-r-j /graphein

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

UpdatedOct 13, 2025
Jupyter Notebook

MolecularNodes

BradyAJohnston /MolecularNodes

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

UpdatedNov 6, 2025
Python

martinpacesa /BindCraft

User friendly and accurate binder design pipeline

design binder protein pyrosetta alphafold2

UpdatedAug 12, 2025
Python

salesforce /progen

Official release of the ProGen models

protein generative-model language-model

UpdatedAug 4, 2023
Python

microsoft /foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

proteins transformer protein diffusion diffusion-models protein-structure-generation

UpdatedDec 12, 2023
Jupyter Notebook

westlake-repl /SaProt

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

protein-structure protein representation-learning protein-sequence predicted-structures pretraining structure-aware protein-language-model alphafold2 foldseek structural-alphbet protein-llm

UpdatedOct 28, 2025
Python

prody /ProDy

A Python Package for Protein Dynamics Analysis

python dynamics protein

UpdatedOct 23, 2025
Python

flowhub-team /awesome-omics

A collection of awesome things regarding all omics.

awesome genomics ngs protein omics single-cell ngs-pipeline wgs-analysis

UpdatedMay 6, 2025

mdshw5 /pyfaidx

Efficient pythonic random access to fasta subsequences

python bioinformatics genomics indexing dna protein fasta samtools bgzf

UpdatedSep 3, 2025
Python

haddocking /pdb-tools

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

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

UpdatedOct 3, 2025
Python

lightdock

lightdock /lightdock

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

UpdatedSep 16, 2025
Python

OATML-Markslab /ProteinGym

Official repository for the ProteinGym benchmarks

benchmark computational-biology protein protein-design protein-fitness

UpdatedJul 21, 2025
HTML

HICAI-ZJU /Scientific-LLM-Survey

Scientific Large Language Models: A Survey on Biological & Chemical Domains

genome text molecule survey protein cell science-research multimodal large-language-models llms sci-llm scientific-languages

UpdatedSep 7, 2025

seqviz

Lattice-Automation /seqviz

a JavaScript DNA, RNA, and protein sequence viewer

biology synthetic-biology vector dna protein rna igem plasmid

UpdatedNov 4, 2025
TypeScript

debbiemarkslab /EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

protein structure-prediction 3d-structure protein-complexes

UpdatedOct 23, 2025
Jupyter Notebook

zjunlp /Mol-Instructions

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

science natural-language-processing resource instructions molecule dataset protein generation llama datasets biomedical instruction instruction-following large-language-models ai-for-science mol-instruction iclr2024

UpdatedOct 28, 2024
Python

AngelRuizMoreno /Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

cheminformatics protein-structure jupyter-notebook computational-biology protein drug-discovery drug-repurposing rdkit openbabel drug-design mdanalysis autodock ledock molecular-docking autodock-vina py3dmol

UpdatedOct 30, 2023
Jupyter Notebook

opendilab /awesome-AI-based-protein-design

A collection of research papers for AI-based protein design

awesome protein-structure artificial-intelligence protein awesome-list

UpdatedMay 13, 2024

a-r-j /ProteinWorkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

benchmark lightning deep-learning protein-structure pytorch dataset protein pretraining

UpdatedApr 27, 2025
Python

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