Biological and Medicinal Chemistry

SBMOpenMM: A Builder of Structure-Based Models for OpenMM

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.


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Supplementary material

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SBMOpenMM - Supplementary - JCIM Revision 1

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