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

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

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!

arpeggia

Calculation of interatomic interactions in molecular structures

protspace

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

rosettapy

A Python utility for wrapping Rosetta command line tools.

mini3di

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

fast-trimul

A drop-in, hardware-agnostic library for Fused Triangle Multiplicative Updates across AlphaFold3-family models, powered by CUTLASS CuTe kernels.

protlabel

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

graphein

Protein Graph Library

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

alphafold-sovereign-mcp

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

molecularnodes

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

protpy

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

pypdb

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

tmap2

Tree-based visualization for high-dimensional data. Organizes similar items into interactive tree structures for any high-dimensional dataset.

stmol

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

atlasfold

Trainable protein folding and co-folding models with a protein language model.

uniprot-mcp-server

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

bionemo-ir

Easy, fast, and memory-efficient structure prediction inference