Improvement of molecular-replacement models withSculptor
Open Access
- 18 March 2011
- journal article
- research article
- Published by International Union of Crystallography (IUCr) in Acta Crystallographica Section D-Biological Crystallography
- Vol. 67 (4), 303-312
- https://doi.org/10.1107/s0907444910051218
Abstract
In molecular replacement, the quality of models can be improved by transferring information contained in sequence alignment to the template structure. A family of algorithms has been developed that make use of the sequence-similarity score calculated from residue-substitution scores smoothed over nearby residues to delete or downweight parts of the model that are unreliable. These algorithms have been implemented in the program Sculptor, together with well established methods that are in common use for model improvement. An analysis of the new algorithms has been performed by studying the effect of algorithm parameters on the quality of models. Benchmarking against existing techniques shows that models from Sculptor compare favourably, especially if the alignment is unreliable. Carrying out multiple trials using alternative models created from the same structure but using different algorithm parameters can significantly improve the success rate.Keywords
This publication has 26 references indexed in Scilit:
- Features and development of CootActa Crystallographica Section D-Biological Crystallography, 2010
- PHENIX: a comprehensive Python-based system for macromolecular structure solutionActa Crystallographica Section D-Biological Crystallography, 2010
- CHAINSAW: a program for mutating pdb files used as templates in molecular replacementJournal of Applied Crystallography, 2008
- BALBES: a molecular-replacement pipelineActa Crystallographica Section D-Biological Crystallography, 2007
- The JCSG MR pipeline: optimized alignments, multiple models and parallel searchesActa Crystallographica Section D-Structural Biology, 2007
- Model preparation inMOLREPand examples of model improvement using X-ray dataActa Crystallographica Section D-Biological Crystallography, 2007
- High-resolution structure prediction and the crystallographic phase problemNature, 2007
- Clustal W and Clustal X version 2.0Bioinformatics, 2007
- Phasercrystallographic softwareJournal of Applied Crystallography, 2007
- FFAS03: a server for profile-profile sequence alignmentsNucleic Acids Research, 2005