Simulated-annealing real-space refinement as a tool in model building

Andrei Korostelev, Richard Bertram, Michael Chapman

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

Methods have been developed that further automate the building of macromolecular structures into electron-density maps. The software supports molecular-dynamics real-space refinement of an atomic model to local regions of a map within the context of a popular molecular-modeling program, O [Jones et al. (1991), Acta Cryst. A47, 110-119]. It is implemented as a module to the CNS refinement package [Brünger et al. (1998), Acta Cryst. D54, 905-921], controlled by a graphical user interface and commands executed directly through the molecular-graphics package. The method is illustrated with examples of the building and rebuilding of protein and nucleic acid models in which laborious manual adjustments are avoided. The resulting models show improved convergence during subsequent reciprocal-space refinement. The novel feature of the RSRef2000 software is the combination of simulated-annealing optimization with local real-space refinement, allowing several local minima to be explored quickly and automatically within the context of interactive model building.

Original languageEnglish (US)
Pages (from-to)761-767
Number of pages7
JournalActa Crystallographica Section D: Biological Crystallography
Volume58
Issue number5
DOIs
StatePublished - 2002
Externally publishedYes

Fingerprint

simulated annealing
Simulated annealing
Software
Molecular Dynamics Simulation
Nucleic Acids
Molecular graphics
Electrons
computer programs
graphical user interface
Molecular modeling
nucleic acids
commands
Graphical user interfaces
Carrier concentration
Molecular dynamics
Proteins
modules
adjusting
molecular dynamics
proteins

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Clinical Biochemistry
  • Structural Biology
  • Condensed Matter Physics

Cite this

Simulated-annealing real-space refinement as a tool in model building. / Korostelev, Andrei; Bertram, Richard; Chapman, Michael.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 58, No. 5, 2002, p. 761-767.

Research output: Contribution to journalArticle

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