Protein Structure Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

gemmi

macromolecular crystallography library and utilities

biopandas

Working with molecular structures in pandas DataFrames

protpy

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

colabfold

Making Protein folding accessible to all!

rosettapy

A Python utility for wrapping Rosetta command line tools.

pyjess

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

stmol

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

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

synth-pdb

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

pypdb

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

graphein

Protein Graph Library

arpeggia

A library for analyzing protein-protein interactions in PDB and mmCIF files

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

mini3di

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

uniprot-mcp-server

Model Context Protocol server for UniProt — Swiss-Prot and TrEMBL protein knowledgebase. 41 tools across 8 families with per-query SHA-256 provenance verification and offline replay.

bio-embeddings

Get protein embeddings from protein sequences

proteinfp

End-to-end protein function prediction from structure alone: active sites, binding pockets, GO terms, PPI partners, and drug candidates.

tape-proteins

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

flatprot

A tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations.

amphipathic

This is a library to evaluate an aminoacid sequence and determine an amphipathic index for each alpha helix or beta sheet.

sidechainnet

An all-atom protein structure dataset for machine learning.

bio-embeddings-tape-proteins

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

diffbio

End-to-end differentiable bioinformatics pipelines built on JAX/Flax NNX