ProDy 1.8 Series

Release Notes

v2.5.0 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.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

ProDy 1.8 Series¶

1.8.2 (Jun 5, 2016)
1.8.1 (May 28, 2016)
1.8 (May 13, 2016)
- MechStiff

1.8.2 (Jun 5, 2016)¶

addCoordset() in PDBEnsemble class, has an additional argument for NMR models.

1.8.1 (May 28, 2016)¶

Bugfixes

getHits() in PDBBlastRecord class, default overlap threshold changed to 0.7 to match with mapOntoChain().

calcModes() in RTB have a bug on number of modes and fixed.

Tab and indentation errors with Python 3.4 are fixed.

1.8 (May 13, 2016)¶

MechStiff ¶

Identification of the weakest/strongest elements of the structure architecture provided together with 3D vizualization and statistics analysis.

Determination of the effective spring constant for selected pair of residues - useful for Single Molecule Force Spectroscopy (SMFS, AFM) and Steered Molecular Dynamics simulations.

Evaluating the contributions of each mode to selected deformations

New Features:

Python 2 and 3 Support

ProDy has been refactored to support Python 2.7 and 3.4. Windows installers for Python 2.7 and 3.4 are available in Installation.

Unit tests are compatible with Python 2.7 and 3.4, and running them with other versions gives errors due to unavailability of some unittest features.