Model preparation in MOLREP and examples of model improvement using X-ray data

TY - JOUR

T1 - Model preparation in MOLREP and examples of model improvement using X-ray data

AU - Lebedev, Andrey A.

AU - Vagin, Alexei A.

AU - Murshudov, Garib N.

PY - 2008/1/4

Y1 - 2008/1/4

N2 - The success of molecular replacement is critically dependent on the quality of the search model. Several model-preparation procedures are integrated in the molecular-replacement program MOLREP. These include model modification on the basis of amino-acid sequence alignment and model correction based on analysis of the solvent-accessibility of the atoms. The packing function used in MOLREP for the translational search is explained in the context of model preparation. In difficult cases, bioinformatics-based modifications are not sufficient for successful molecular replacement. An approach implemented in MOLREP for solving cases with translational noncrystallographic symmetry is an example of model preparation in which analysis of X-ray data plays an essential role. In addition, two examples are presented in which the X-ray data were used to refine partial models for subsequent use in molecular replacement.

AB - The success of molecular replacement is critically dependent on the quality of the search model. Several model-preparation procedures are integrated in the molecular-replacement program MOLREP. These include model modification on the basis of amino-acid sequence alignment and model correction based on analysis of the solvent-accessibility of the atoms. The packing function used in MOLREP for the translational search is explained in the context of model preparation. In difficult cases, bioinformatics-based modifications are not sufficient for successful molecular replacement. An approach implemented in MOLREP for solving cases with translational noncrystallographic symmetry is an example of model preparation in which analysis of X-ray data plays an essential role. In addition, two examples are presented in which the X-ray data were used to refine partial models for subsequent use in molecular replacement.

KW - MOLECULAR-REPLACEMENT

KW - MAXIMUM-LIKELIHOOD

KW - PROTEINS

KW - PIPELINE

KW - REFINEMENT

KW - GENERATION

KW - ALIGNMENT

KW - SEARCH

KW - SERVER

UR - http://www.scopus.com/inward/record.url?scp=37349121133&partnerID=8YFLogxK

U2 - 10.1107/S0907444907049839

DO - 10.1107/S0907444907049839

M3 - Article

SN - 0907-4449

VL - 64

SP - 33

EP - 39

JO - Acta Crystallographica. Section D, Biological Crystallography

JF - Acta Crystallographica. Section D, Biological Crystallography

IS - 1

ER -