ProDy 2.0 Series
- 2.0 (Dec 30, 2020)

Release Notes

v2.0 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

ProDy 2.0 Series¶

2.0 (Dec 30, 2020)

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.