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