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Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):464-8.

Real-space molecular-dynamics structure refinement.

Author information

1
Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.

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.

PMID:
10089356
[Indexed for MEDLINE]

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