Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions

M. Dixit, S. Das, A. R. Mhashal, R. Eitan, D. T. Major

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

11 Scopus citations

Abstract

This chapter aims to present some basic multiscale approaches available for enzyme simulations, and to point out practical details and pitfalls that are not often discussed in the literature, but can greatly influence the outcome of any in silico enzyme study. We cover principle methodological steps of multiscale studies of general enzyme reactions. This includes choice of starting structures, boundary conditions, potential energy surfaces, reaction coordinates, simulation methods, as well as the choice of method for the treatment of nuclear quantum effects. Together, these and additional steps are crucial for the success of enzyme-modeling projects and should be considered prior to embarking on multiscale modeling.

Original languageEnglish
Title of host publicationMethods in Enzymology
EditorsGregory A. Voth
PublisherAcademic Press Inc.
Pages251-286
Number of pages36
ISBN (Print)9780128053478
DOIs
StatePublished - 2016

Publication series

NameMethods in Enzymology
Volume577
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Bibliographical note

Publisher Copyright:
© 2016 Elsevier Inc.

Keywords

  • Enzyme modeling
  • Multiscale modeling
  • Nuclear quantum effect
  • Path-integral
  • Potential energy surface
  • Quantum mechanics-molecular mechanics

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