Protein Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

pyfaidx

Efficient pythonic random access to fasta subsequences

pdb-tools

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

prody

A Python Package for Protein Dynamics Analysis

prospr

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

seqtree

Efficiently search and cluster highly similar short sequences

peptacular

Parse ProForma 2.1 peptide sequences and calculate masses, fragments, and isotopic distributions in Python.

icn3dpy

web-based protein structure viewer and analysis tool interactively or in batch mode

orfipy

Fast and flexible ORF finder

peptides

Physicochemical properties, indices and descriptors for amino-acid sequences.

rosettapy

A Python utility for wrapping Rosetta command line tools.

graphein

Protein Graph Library

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

molecularnodes

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

psimodpy

Python library, API, and MCP server for the PSI-MOD protein modification ontology

unimodpy

Python library, API, and MCP server for the UNIMOD mass spectrometry modifications database

pefftacular

Python library for reading and writing PEFF (PSI Extended FASTA Format) files. PEFF is a superset of FASTA used in proteomics that carries rich per-entry annotations.

uniprotptmpy

Python library, API, and MCP server for the UniProt PTM controlled vocabulary

esm2quinox

An implementation of ESM2 in Equinox+JAX

pantometry

Physics for simulated worlds in Rust: a kernel that knows no domain and thirteen that do — heat, mechanics, optics, acoustics, electromagnetism, elasticity, fluids, porous media, molecular dynamics, electrical, quantum, pharmacokinetics, protein folds — plus scene and view layers that know none. Dimensions in the types, conservation audited.

proxide

High-performance protein I/O and physics bridging for JAX, with a Rust backend for structure parsing and force-field parameterization

proteinmotion

Animate proteins, DNA, and RNA in Python with a Manim-inspired API, native GPU rendering, and Blender EEVEE.

uniprot-mcp-server

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

dualis

Physics for simulated worlds in Rust: a kernel that knows no domain and thirteen that do — heat, mechanics, optics, acoustics, electromagnetism, elasticity, fluids, porous media, molecular dynamics, electrical, quantum, pharmacokinetics, protein folds — plus scene and view layers that know none. Dimensions in the types, conservation audited.