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.

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.

rosettapy

A Python utility for wrapping Rosetta command line tools.

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

peptides

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

synth-pdb

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

graphein

Protein Graph Library

icn3dpy

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

orfipy

Fast and flexible ORF finder

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.

flatprot

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

esm2quinox

An implementation of ESM2 in Equinox+JAX

pyxlms

A python package to process protein cross-linking data.

chilife

Python package for site-directed spin labeling of proteins

covdrugsim

Package to automate quantum mechanical calculations and molecular dynamics simulations of covalent drugs.

agfusion

Python package to annotate and visualize gene fusions.

biobase

A comprehensive package of biological constants, serving as a foundational resource for biology and bioinformatics, complemented by functions to streamline related tasks.

rosetta-finder

Searching for Rosetta Binaries.

pixelgen-pixelator

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

cogclassifier

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

biocentral-api

Programmatic access to the biocentral ecosystem.