Proteins Python Packages

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

fpbase

Python wrapper for FPBase.org GraphQL API.

pykvfinder

pyKVFinder: Python-C parallel KVFinder

haddock3

Official repo of the modular BioExcel version of HADDOCK

molecularnodes

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

pypdb

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

greedyfas

FAS - Tool for Feature Architecture Similarity calculation

bio2bel-kegg

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

biotrainer

Biological prediction models made simple.

seqme

Metrics for evaluating biological sequence design

cpiextract

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

progen-transformer

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

afpropred

AfProPred: A tool to predict anti-freezing proteins

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.

bigecyhmm

Predict enzymatic impact on biogeochemical cycles from proteomes.

protify

Low code molecular property prediction

deepinteract

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

protviewer

A tool to view activity pattern in protein structures.

correlationplus

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

geometricus

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

pyprotein

Does basic calculations on polypeptides/proteins/enzymes, like the isoelectric point, the charge, the molar mass, the mean residue molar mass, the elemental composition, and the nitrogen content.

prothash

Fast protein sequence embeddings distilled from ESMC.

bio2bel-interpro

A Bio2BEL package for converting InterPro to BEL