Protein Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

pyfaidx

Efficient pythonic random access to fasta subsequences

prody

A Python Package for Protein Dynamics Analysis

pdb-tools

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

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

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.

esm2quinox

An implementation of ESM2 in Equinox+JAX

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..

seqtree

Efficient search for highly similar short sequences

peptides

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

uniprot-mcp-server

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

graphein

Protein Graph Library

rosettapy

A Python utility for wrapping Rosetta command line tools.

icn3dpy

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

pyxlms

A python package to process protein cross-linking data.

bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

pixelgen-pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

flatprot

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

orfipy

Fast and flexible ORF finder

mercat2

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

molecularnodes

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

peptacular

A Python package for peptide sequence analysis built around ProForma 2.1 notation. Calculate masses, generate fragments, predict isotopic patterns, and more.

chilife

Python package for site-directed spin labeling of proteins

cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category