Computing ensembles of transitions with molecular dynamics simulations

Juan R. Perilla, Thomas B Woolf

Research output: Contribution to journalArticle

Abstract

A molecular understanding of conformational change is important for connecting structure and function. Without the ability to sample on the meaningful large-scale conformational changes, the ability to infer biological function and to understand the effect of mutations and changes in environment is not possible. Our Dynamic Importance Sampling method (DIMS), part of the CHARMM simulation package, is a method that enables sampling over ensembles of transition intermediates. This chapter outlines the context for the method and the usage within the program.

Original languageEnglish (US)
Pages (from-to)237-252
Number of pages16
JournalMethods in molecular biology (Clifton, N.J.)
Volume1215
DOIs
StatePublished - 2015

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Molecular Dynamics Simulation
Mutation

Keywords

  • Conformational transition
  • Relative free energy
  • Sampling intermediates
  • Statistical mechanics of proteins
  • Structure–function

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Medicine(all)

Cite this

Computing ensembles of transitions with molecular dynamics simulations. / Perilla, Juan R.; Woolf, Thomas B.

In: Methods in molecular biology (Clifton, N.J.), Vol. 1215, 2015, p. 237-252.

Research output: Contribution to journalArticle

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