Computing ensembles of transitions with molecular dynamics simulations

Juan R. Perilla, Thomas B. Woolf

Research output: Chapter in Book/Report/Conference proceedingChapter

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)
Title of host publicationMolecular Modeling of Proteins
Subtitle of host publicationSecond Edition
PublisherSpringer Fachmedien
Pages237-252
Number of pages16
ISBN (Electronic)9781493914654
ISBN (Print)9781493914647
DOIs
StatePublished - Oct 20 2014

Keywords

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

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Medicine(all)

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    Perilla, J. R., & Woolf, T. B. (2014). Computing ensembles of transitions with molecular dynamics simulations. In Molecular Modeling of Proteins: Second Edition (pp. 237-252). Springer Fachmedien. https://doi.org/10.1007/978-1-4939-1465-4_11