Protein Structure Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

8.5M 5K 2K

gemmi

macromolecular crystallography library and utilities

799K 348 57

biopandas

Working with molecular structures in pandas DataFrames

35K 751 117

pyjess

Cython bindings and Python interface to Jess, a 3D template matching software for protein structures. Now 10x faster!

21K 10 0

protpy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

18K 17 1

stmol

This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.

8K 211 37

colabfold

Making Protein folding accessible to all!

8K 3K 715

rosettapy

A Python utility for wrapping Rosetta command line tools.

7K 1 0

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

5K 335 76

graphein

Protein Graph Library

5K 1K 140

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development

4K 1 0

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361

4K 676 141

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

4K 34 1

mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

4K 80 4

arpeggia

Calculation of interatomic interactions in molecular structures

3K 4 1

pdbe-arpeggio

Arpeggio calculates interatomic contacts based on the rules defined in CREDO.

2K 126 23

mdeepfri

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

2K 45 7

tape-proteins

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

2K 739 135