SBMOpenMM: A Builder of Structure-Based Models for OpenMM

12 May 2021, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

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.


Keywords

Structure-Based Models
Molecular dynamics
Protein folding
SBMOpenMM
OpenMM

Supplementary materials

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Description
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Title
SBMOpenMM - Supplementary - JCIM Revision 1
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Supplementary weblinks

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