ProDy 2.0 Series

2.0 (Dec 30, 2020)

New Features:


  • New classes and functions for Essential Site Scanning Analysis (ESSA)

Updates for CryoDy

  • Finalised the AdaptiveANM (initially added in v1.10.11) for exploring transitions between conformations.
  • Improved domain decomposition

Expanded database module

  • New interfaces including for QuartataWeb

New compounds module

  • New modules for fetching and parsing compound data from the PDB including Biologically Interesting Reference Dictionary (BIRD) and Chemical Component Dictionary (CCD) CIF files
  • New functions module including 2D chemical similarity calculations using Morgan Fingerprint Similarity.

Improved membrane ENMs

  • New implementation of exANM based on iterative Schur complements and block-wise inversion
  • New exGNM based on improved exANM

Bug Fixes and Improvements:

  • New function inferBonds() in AtomGroup for inferring bonds based on distances without information from PSF files.