Real-space molecular-dynamics structure refinement

Zhi Chen, Eric Blanc, Michael Chapman

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.

Original languageEnglish (US)
Pages (from-to)464-468
Number of pages5
JournalActa Crystallographica Section D: Biological Crystallography
Volume55
Issue number2
DOIs
StatePublished - Feb 1999
Externally publishedYes

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Molecular Dynamics Simulation
Molecular Structure
Molecular dynamics
molecular dynamics
Least-Squares Analysis
Torsional stress
Maximum likelihood
Diffraction
escape
torsion
optimization
diffraction

ASJC Scopus subject areas

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

Cite this

Real-space molecular-dynamics structure refinement. / Chen, Zhi; Blanc, Eric; Chapman, Michael.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 55, No. 2, 02.1999, p. 464-468.

Research output: Contribution to journalArticle

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