Protein Analysis Python Packages

pdbe-arpeggio

Calculation of interatomic interactions in molecular structures

protclust

protclust is a Python library for protein sequence analysis that integrates MMseqs2 for fast clustering and provides tools for creating robust machine learning datasets. It offers cluster-aware data splitting to prevent sequence similarity bias in model evaluation, along with comprehensive protein embedding capabilities for feature generation.

sinatra-pro

Topological data analytic approach for discovering biophysical signatures in protein dynamics

speadi

A Python package that aims to characterise the dynamics of local chemical environments from Molecular Dynamics trajectories of proteins and other biomolecules. Public mirror of https://gitlab.jsc.fz-juelich.de/slbio/speadi.

parylation-predictor

ParylationPredictor — predict PARylation sites and detect PAR-binding domains in proteins. Publication-quality 8-panel figures, Excel, HTML report, JSON/TSV exports.

mmseqspy

protclust is a Python library for protein sequence analysis that integrates MMseqs2 for fast clustering and provides tools for creating robust machine learning datasets. It offers cluster-aware data splitting to prevent sequence similarity bias in model evaluation, along with comprehensive protein embedding capabilities for feature generation.