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SBMOpenMM: A Builder of Structure-Based Models for OpenMM

preprint
submitted on 29.01.2021, 09:49 and posted on 01.02.2021, 06:47 by Martin Floor, Kengjie Li, Miquel Estévez-Gay, Luis Agulló, Pau Marc Muñoz, Jenn-Kang Hwang, Sílvia Osuna, Jordi Villà-Freixa

Here we introduce SBMOpenMM, a python library to build Structure-Based Models (SBMs), that uses the OpenMM framework to create and run SBM simulations. The code is flexible, user-friendly, and profits from high customizability and GPU performance provided by the OpenMM platform. We demonstrate its use in the evaluation of the two-step folding process of FoxP1 transcription factor protein. Our results indicate that the newly developed SBM can be successfully applied to elucidating the underlying mechanisms of biomolecular processes.


History

Email Address of Submitting Author

mfloor@uic.es

Institution

Universitat Internacional de Catalunya

Country

Spain

ORCID For Submitting Author

0000-0001-8453-0815

Declaration of Conflict of Interest

No conflict of interest

Version Notes

Initial submission

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ChemRxiv

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