Path-sampling strategies for simulating rare events in biomolecular systems

Lillian T. Chong, Ali S. Saglam, Daniel M. Zuckerman

Research output: Contribution to journalReview articlepeer-review

39 Scopus citations

Abstract

Despite more than three decades of effort with molecular dynamics simulations, long-timescale (ms and beyond) biologically relevant phenomena remain out of reach in most systems of interest. This is largely because important transitions, such as conformational changes and (un)binding events, tend to be rare for conventional simulations (<10 μs). That is, conventional simulations will predominantly dwell in metastable states instead of making large transitions in complex biomolecular energy landscapes. In contrast, path sampling approaches focus computing effort specifically on transitions of interest. Such approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.

Original languageEnglish (US)
Pages (from-to)88-94
Number of pages7
JournalCurrent Opinion in Structural Biology
Volume43
DOIs
StatePublished - Apr 1 2017

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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