Proteins Python Packages

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

pypdb

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

fpbase

Python wrapper for FPBase.org GraphQL API.

haddock3

Official repo of the modular BioExcel version of HADDOCK

greedyfas

FAS - Tool for Feature Architecture Similarity calculation

progen-transformer

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

bio2bel-kegg

A package for converting KEGG gene sets into BEL

molecularnodes

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

cpiextract

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

geom3d

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

afpropred

AfProPred: A tool to predict anti-freezing proteins

seqme

Metrics for evaluating biological sequence design

kif

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

dips-plus

The Enhanced Database of Interacting Protein Structures for Interface Prediction

deepinteract

A geometric deep learning framework (Geometric Transformers) for predicting protein interface contacts. (ICLR 2022)

biotrainer

Biological prediction models made simple.

protify

Low code molecular property prediction

protviewer

A tool to view activity pattern in protein structures.

correlationplus

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

omnipath-utils

ID translation, taxonomy, orthology and reference lists for molecular biology

geometricus

A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

bigecyhmm

Predict biogeochemical cycles from protein fasta files.

bio2bel-interpro

A Bio2BEL package for converting InterPro to BEL

networker

A python package to generate and analyse protein similarity networks.