Modeling and simulating biomolecules

Research output: Contribution to journalArticle

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)
JournalFASEB Journal
Volume11
Issue number9
StatePublished - 1997

Fingerprint

molecular dynamics
Biomolecules
Molecular dynamics
Molecular Dynamics Simulation
Protein folding
protein folding
Equations of motion
ears
Protein Folding
methodology
Sampling
Ear
Atoms
energy
Computer simulation
sampling

ASJC Scopus subject areas

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

Cite this

Modeling and simulating biomolecules. / Schlick, Tamar.

In: FASEB Journal, Vol. 11, No. 9, 1997.

Research output: Contribution to journalArticle

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