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.

ANMD simulations¶

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runANMD(atoms, num_modes=2, max_rmsd=2.0, num_steps=5, tolerance=10.0, **kwargs)[source]¶

Runs the ANMD hybrid simulation method ([CM22]), which generates conformations along single modes using traverseModes() and minimises them.

The first non-zero mode is scaled to max_rmsd and the remaining modes are scaled accordingly using their eigenvalues.

kwargs of traverseMode can be provided: pos, neg and reverse

Parameters:

Parameters:	atoms (`Atomic`) – an object with atom and coordinate data. This should be a complete atomic model. It is ok to be missing some side chain atoms and hydrogens, but not fragments, such as loops. num_modes (int) – number of modes to calculate Default is 2 max_rmsd (float) – maximum rmsd for non-zero mode 1 Default is 2. num_steps (int) – number of conformers in each direction for each mode Default is 5 tolerance (float) – tolerance for energy minimisation in OpenMM in kilojoule/mole/nanometer. Default is 10 as in OpenMM skip_modes (int) – number of modes to skip Default is 0 anm (`NMA`, `ANM`, `ModeSet`) – your own NMA modes or ModeSet to use instead Default is None

atoms (Atomic) – an object with atom and coordinate data. This should be a complete atomic model. It is ok to be missing some side chain atoms and hydrogens, but not fragments, such as loops.
num_modes (int) – number of modes to calculate Default is 2
max_rmsd (float) – maximum rmsd for non-zero mode 1 Default is 2.
num_steps (int) – number of conformers in each direction for each mode Default is 5
tolerance (float) – tolerance for energy minimisation in OpenMM in kilojoule/mole/nanometer. Default is 10 as in OpenMM
skip_modes (int) – number of modes to skip Default is 0
anm (NMA, ANM, ModeSet) – your own NMA modes or ModeSet to use instead Default is None

[CM22]

Mary Hongying Cheng, James M Krieger, Anupam Banerjee, Yufei Xiang, Burak Kaynak, Yi Shi, Moshe Arditi, Ivet Bahar. Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. iScience 2022 25(3):103939.