Computing ensembles of transitions with molecular dynamics simulations

Juan R. Perilla; Thomas B. Woolf

doi:10.1007/978-1-4939-1465-4_11

Computing ensembles of transitions with molecular dynamics simulations

Juan R. Perilla, Thomas B. Woolf

School of Medicine

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2 Scopus citations

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 language	English (US)
Title of host publication	Molecular Modeling of Proteins
Subtitle of host publication	Second Edition
Publisher	Springer Fachmedien
Pages	237-252
Number of pages	16
ISBN (Electronic)	9781493914654
ISBN (Print)	9781493914647
DOIs	https://doi.org/10.1007/978-1-4939-1465-4_11
State	Published - Oct 20 2014

Keywords

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

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences
General Medicine

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10.1007/978-1-4939-1465-4_11

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Computing ensembles of transitions with molecular dynamics simulations

Abstract

Keywords

ASJC Scopus subject areas

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