Modeling and simulating biomolecules

Research output: Contribution to journalArticlepeer-review

Abstract

The importance of biomolocular modeling and simulations is steadily increasing with progress in experimental techniques, algorithm development, and now computing (ethnologies. Otic of the major problems in the field involves inadequate contigurational sampling. This encompasses both the multiple minima problem in energy minimization and the tirnestep problem in molecular dynamics. In molecular dynamics simulations, atomic motion is propagated through numerical integration of the classical equations of motion. In theory, molecular dynamics can bridge the spatial and temporal resolution and thus capture molecular motion over a. wide range of thermally accessible states. In practice, typical all-atom models and standard integration methods limit our trajecto ries to short-time processes compared to the motion of major interest (e.g., protein folding). Thus, a variety of methods on different spatial and temporal scales must be devised to address important biological questions. These computational problems and some current approaches to them will be described in this broad introductory talk.

Original languageEnglish (US)
Pages (from-to)A1123
JournalFASEB Journal
Volume11
Issue number9
StatePublished - 1997

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Genetics

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