Proteins Python Packages

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

pypdb

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

greedyfas

FAS - Tool for Feature Architecture Similarity calculation

fpbase

Python wrapper for FPBase.org GraphQL API.

haddock3

Official repo of the modular BioExcel version of HADDOCK

progen-transformer

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

cpiextract

CPIExtract is a software package to collect and harmonize small molecule and protein interactions with support for stereoisomer matching.

molecularnodes

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

seqme

Metrics for evaluating biological sequence design

bio2bel-kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

afpropred

A tool to predict anti-freezing proteins

omnipath-utils

Prior-knowledge processing utilities Python package, database and web API

dips-plus

The Enhanced Database of Interacting Protein Structures for Interface Prediction

kif

KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.

deepinteract

A geometric deep learning pipeline for predicting protein interface contacts.

biotrainer

Biological prediction models made simple.

protify

Low code molecular property prediction

protviewer

A tool to view activity pattern in protein structures.

geometricus

Fast, structure-based, alignment-free protein embedding

correlationplus

A Python package to calculate, visualize and analyze correlation maps of proteins.

bigecyhmm

Predict enzymatic impact on biogeochemical cycles from proteomes.

bio2bel-interpro

A Bio2BEL package for converting InterPro to BEL

folding

AlphaFold2 protein predictions

idpflex

Analysis of intrinsically disordered proteins by comparing MD simulations to Small Angle Scattering experiments