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

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

protpy

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

bio-embeddings

Get protein embeddings from protein sequences

colabfold

Making Protein folding accessible to all!

pyjess

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

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

stmol

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

arpeggia

Calculation of interatomic interactions in molecular structures

pypdb

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

alphafold-sovereign-mcp

Local-first biomedical MCP over AlphaFold DB + 8 public sources, with SQLite knowledge graph, offline mode, and explicit clinical-use limits.

uniprot-mcp-server

Auditable UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.

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

graphein

Protein Graph Library

rosettapy

A Python utility for wrapping Rosetta command line tools.

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.

sidechainnet

An all-atom protein structure dataset for machine learning.

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

mini3di

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

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

Python package for creating simplified 2D protein visualizations. Specialized on showing differences and similarities between proteins of the same protein family.

molecularnodes

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