phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta

• Published in: Journal of structural and functional genomics Vol. 13; no. 2; pp. 81 - 90
• Main Authors: Terwilliger, Thomas C., DiMaio, Frank, Read, Randy J., Baker, David, Bunkóczi, Gábor, Adams, Paul D., Grosse-Kunstleve, Ralf W., Afonine, Pavel V., Echols, Nathaniel
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.06.2012; Springer Nature B.V
• Subjects: Algorithms; Automation; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Computational Biology - methods; Crystallography; Crystallography, X-Ray - methods; Databases, Protein; Forestry Management; Human Genetics; Internet; Laboratories; Licenses; Life Sciences; Macromolecular Substances - chemistry; Magnetic Resonance Spectroscopy; Microbial Genetics and Genomics; Models, Molecular; Molecular modelling; Plant Genetics and Genomics; Protein Conformation; Proteins - analysis; Proteins - chemistry; Proteomics - methods; Software; Structure-function relationships; Macromolecular crystallography; Molecular replacement; Automation
• ISSN: 1345-711X; 1570-0267
• DOI: 10.1007/s10969-012-9129-3

The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement.