Iterative model building, structure refinement and density modification with thePHENIX AutoBuildwizard
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Open Access
- 4 December 2007
- journal article
- research article
- Published by International Union of Crystallography (IUCr) in Acta Crystallographica Section D-Biological Crystallography
- Vol. 64 (1) , 61-69
- https://doi.org/10.1107/s090744490705024x
Abstract
The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.Keywords
This publication has 19 references indexed in Scilit:
- A probabilistic approach to protein backbone tracing in electron density mapsBioinformatics, 2006
- Crystallographic Refinement by Knowledge-Based Exploration of Complex Energy LandscapesStructure, 2005
- A robust bulk-solvent correction and anisotropic scaling procedureActa Crystallographica Section D-Biological Crystallography, 2005
- Likelihood-enhanced fast translation functionsActa Crystallographica Section D-Biological Crystallography, 2005
- Identification of common molecular subsequencesPublished by Elsevier ,2004
- Likelihood-enhanced fast rotation functionsActa Crystallographica Section D-Biological Crystallography, 2004
- Statistical density modification using local pattern matchingActa Crystallographica Section D-Biological Crystallography, 2003
- Automated main-chain model building by template matching and iterative fragment extensionActa Crystallographica Section D-Biological Crystallography, 2002
- Statistical density modification with non-crystallographic symmetryActa Crystallographica Section D-Biological Crystallography, 2002
- A general method applicable to the search for similarities in the amino acid sequence of two proteinsJournal of Molecular Biology, 1970