Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps

Xiongwu Wu, Sriram Subramaniam, David A. Case, Katherine W. Wu, Bernard R. Brooks

Research output: Contribution to journalArticle

Abstract

We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy.

Original languageEnglish (US)
Pages (from-to)429-440
Number of pages12
JournalJournal of Structural Biology
Volume183
Issue number3
DOIs
StatePublished - Sep 2013
Externally publishedYes

Keywords

  • Electron microscopy
  • Flexible fitting
  • Map-restraint
  • Self-guided Langevin dynamics
  • Targeted conformational search

ASJC Scopus subject areas

  • Structural Biology

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