ProDy 2.5 Series

2.5.0 (Aug 14, 2024)

New Features:

  • InSty module prody/proteins/interactions.py for protein interactions and stability

  • WatFinder module prody/proteins/waterbridges.py for analysing water bridges, chains and clusters

  • Membrane exANM and exGNM apps

  • kmedoid clustering

  • Logistic regression for differences between sub-ensembles

  • MMTF Parser by @vratins

  • Protein-ligand interactions including calcSminaBindingAffinity by @karolamik13

  • New support for Interpro Pfam

  • New modules for accessing Bioexcel cv19 simulation database (precursor to MDDB)

Bug Fixes and Improvements:

  • add weights to showProjection and fix colors

  • fix catdcd frame selection

  • fix showAtomicLines gaps

  • update pyproject.toml and setup.py to limit scipy

  • fix clustenm saving and loading

  • fix adp matrix by @jamesmkrieger

  • several fixes related to fetching, parsing and writing pdb and cif files

  • limit pyparsing<=3.1.1

New Contributors:

Full Changelog: https://github.com/prody/ProDy/compare/v2.4.1…v2.5.0