Protein Protein Interaction Python Packages

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

arpeggia

Calculation of interatomic interactions in molecular structures

uniprot-mcp-server

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

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

duello

Osmotic second virial coefficient (𝐵₂) and dissociation constant (𝐾𝑑) for two rigid macromolecules

contact-map

Contact maps based on MDTraj

nease

A network-based approach for exon set enrichment

spada

Find splicing-led, functional changes of the proteome.

protify

Low code molecular property prediction

deeprank

This repository has been integrated in https://github.com/DeepRank/deeprank2

mmtfpyspark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

mdinteractions

A python package for the distance-based analysis of intra- and inter-protein interactions

pedl

Search the biomedical literature for protein interactions andprotein associations.

ppi-net-builder

Protein-Protein Interaction (PPI) network construction and analysis in Python

acrcasppi-ml

Prediction of protein-protein interaction between anti-crispr protein (acr) and CRISPR-associated (cas) protein using machine learning algorithm

ymap

An automated method to map yeast variants to proteins modifications and functional regions

ppi-origami

Tools for processing and analysing PPI datasets

splitpea

Splitpea: method for calculating network rewiring changes due to splicing

farseernmr

A software suite for automatic treatment, analysis and plotting of large and multivariable datasets of bioNMR peaklists.

braid-mrf

Predicting protein complexes

ppaxe

Protein-Protein interactions extractor from PubMed articles

intrepppid

Incorporating Triplet Error for Predicting PPIs using Deep Learning

pyscorpion

Constructs cell-type-specific gene regulatory networks from single-cell RNA-sequencing data using the SCORPION algorithm, which aggregates cells into super-cells and applies PANDA to infer transcription factor-target regulatory relationships.