phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta
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...
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| Published in | Journal of structural and functional genomics Vol. 13; no. 2; pp. 81 - 90 |
|---|---|
| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Dordrecht
Springer Netherlands
01.06.2012
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1345-711X 1570-0267 1570-0267 |
| DOI | 10.1007/s10969-012-9129-3 |
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| Abstract | 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. |
|---|---|
| AbstractList | 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. Issue Title: Special Issue: International Conference on Structural Genomics, 2011 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.[PUBLICATION ABSTRACT] 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. 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.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. |
| Author | Baker, David Read, Randy J. Grosse-Kunstleve, Ralf W. Bunkóczi, Gábor Adams, Paul D. DiMaio, Frank Afonine, Pavel V. Echols, Nathaniel Terwilliger, Thomas C. |
| Author_xml | – sequence: 1 givenname: Thomas C. surname: Terwilliger fullname: Terwilliger, Thomas C. email: terwilliger1@earthlink.net organization: Los Alamos Institutes and BioScience Division, Los Alamos National Laboratory – sequence: 2 givenname: Frank surname: DiMaio fullname: DiMaio, Frank organization: Department of Biochemistry, University of Washington – sequence: 3 givenname: Randy J. surname: Read fullname: Read, Randy J. organization: Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge – sequence: 4 givenname: David surname: Baker fullname: Baker, David organization: Department of Biochemistry, University of Washington – sequence: 5 givenname: Gábor surname: Bunkóczi fullname: Bunkóczi, Gábor organization: Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge – sequence: 6 givenname: Paul D. surname: Adams fullname: Adams, Paul D. organization: Lawrence Berkeley National Laboratory – sequence: 7 givenname: Ralf W. surname: Grosse-Kunstleve fullname: Grosse-Kunstleve, Ralf W. organization: Lawrence Berkeley National Laboratory – sequence: 8 givenname: Pavel V. surname: Afonine fullname: Afonine, Pavel V. organization: Lawrence Berkeley National Laboratory – sequence: 9 givenname: Nathaniel surname: Echols fullname: Echols, Nathaniel organization: Lawrence Berkeley National Laboratory |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22418934$$D View this record in MEDLINE/PubMed |
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| Copyright | The Author(s) 2012 Springer Science+Business Media B.V. 2012 |
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| Keywords | Macromolecular crystallography Molecular replacement Automation |
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electron density mapsActa Cryst2001D57101310191:CAS:528:DC%2BD3MXksVyrsLg%3D EvansPMcCoyAAn introduction to molecular replacementActa Cryst2008D641101:CAS:528:DC%2BD2sXhsVGjt7jL BakerMLJuTChiuWIdentification of secondary structure elements in intermediate resolution density mapsStructure2007157191722352810.1016/j.str.2006.11.0081:CAS:528:DC%2BD2sXmtVentw%3D%3D KovalevskyAYLiuFLeshchenkoSGhoshAKLouisJMHarrisonRWWeberITUltra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114J Mol Biol20063631611731696213610.1016/j.jmb.2006.08.0071:CAS:528:DC%2BD28XpvFSitLY%3D Stokes-ReesISlizPProtein structure determination by exhaustive search of Protein Data Bank derived databasesProc Natl Acad Sci USA201010721476214812109830610.1073/pnas.10120951071:CAS:528:DC%2BC3cXhs1WisL7P TerwilligerTCStatistical density modification with non-crystallographic symmetryActa Cryst2002D58208220861:CAS:528:DC%2BD3sXkslymtw%3D%3D RoversiPBlancEVonrheinCEvansGBricogneGRefinement of severely incomplete structures with maximum likelihood in BUSTER-TNTActa Cryst2000D56131613231:CAS:528:DC%2BD3cXnsFart7s%3D TC Terwilliger (9129_CR36) 2002; D58 TJ Oldfield (9129_CR25) 2002; D58 F DiMaio (9129_CR28) 2011; 473 B Qian (9129_CR29) 2007; 450 F DiMaio (9129_CR37) 2009; 392 RM Keegan (9129_CR8) 2011; D67 M Delarue (9129_CR10) 2008; D64 AY Kovalevsky (9129_CR40) 2006; 363 HM Berman (9129_CR3) 2000; 28 B Mao (9129_CR6) 2011; 19 R Schwarzenbacher (9129_CR7) 2004; 60 AJ McCoy (9129_CR14) 2007; 40 TC Terwilliger (9129_CR16) 2004; D60 PD Adams (9129_CR32) 2010; D66 TA Ramelot (9129_CR30) 2009; 75 9129_CR18 R Das (9129_CR31) 2009; D65 D Chivian (9129_CR34) 2003; 53 G Schröder (9129_CR41) 2010; 464 G Langer (9129_CR17) 2008; 3 TC Terwilliger (9129_CR19) 2008; 64 9129_CR35 MG Rossmann (9129_CR1) 1972 TJ Oldfield (9129_CR26) 2003; D59 9129_CR42 F DiMaio (9129_CR22) 2007; 23 J Söding (9129_CR33) 2005; 21 K Cowtan (9129_CR21) 2006; D62 M Li (9129_CR39) 2011; 18 P Roversi (9129_CR15) 2000; D56 A Lyskowski (9129_CR38) 2011; F67 YW Chen (9129_CR4) 2000; 8 A Kidera (9129_CR11) 1992; 225 F Long (9129_CR12) 2008; D64 ML Baker (9129_CR20) 2007; 15 P Evans (9129_CR2) 2008; D64 RJ Read (9129_CR9) 2001; 57 DG Levitt (9129_CR24) 2001; D57 TC Terwilliger (9129_CR27) 2010; D66 G Bunkoczi (9129_CR5) 2010; D67 I Stokes-Rees (9129_CR13) 2010; 107 TR Ioerger (9129_CR23) 2003; 374 |
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| Title | phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta |
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