ProDy 2.0 Series

2.0.2 (February 17, 2022)

New Features:

structures

and the frames sampled over the time course of a simulation or the conformers in an ensemble.

  • Updates to ClustENM(D) to use latest and more efficient OpenMM version, 7.6
  • New :function:`.parseGromacsModes` for parsing NMA and PCA modes calculated in Gromacs,

allowing the use of all-atom force fields and more efficient handling of large trajectories

Bug Fixes and Improvements:

  • Bug fixes to searchPfam and fetchPfamMSA, which no longer worked due to some security change.
  • Bug fix to Ensembles and Conformations for weights being indexed twice
  • Bug fix to –quiet option of apps that fixes the VMD ProDy interface
  • General documentation and error improvements

Full Changelog: https://github.com/prody/ProDy/compare/v2.0.1...v2.0.2

2.0.1 (Dec 20, 2021)

New Features:

to TEMPy objects, allowing calculations such as cross-correlation coefficient (CCC) to EM maps.

for further interpretation of PRS results.

  • Reinstated the option of using forces in PRS as in ProDy v1.8 (turbo=**False**)
  • Added GitHub Actions Continuous Integration in place of Travis.

Bug Fixes and Improvements:

  • Compatibility and bug fixes for various functions, including pyparsing for selections.
  • Extended AdaptiveANM to work with other models including explicit membrane

ANM, exANM.

  • Improved capabilities for fetching and parsing mmCIF and EMD files.
  • Improved handling of residue and serial numbers including hexadecimal and hybrid36 formats.
  • Consistency fixes.
  • More non-standard amino acids (MEN, CSB, CME).

Full Changelog: https://github.com/prody/ProDy/compare/v2.0...v2.0.1

2.0 (Dec 30, 2020)

New Features:

ESSA

  • 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.