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ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

ABSTRACT: Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates.

SUBMITTER: Parvatikar A

PROVIDER: S-EPMC5961460 | biostudies-other | 2018 May

REPOSITORIES: biostudies-other

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ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

Parvatikar Akash A Vacaliuc Gabriel S GS Ramanathan Arvind A Chennubhotla S Chakra SC

Biophysical journal 20180501 9

Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations ...[more]

PMID: 29742397

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