title: Structure prediction for CASP8 with all-atom refinement using Rosetta.
abstract: We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Srivatsan
authors.initials: S
authors.lastname: Raman
authors.forename: Robert
authors.initials: R
authors.lastname: Vernon
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.forename: Michael
authors.initials: M
authors.lastname: Tyka
authors.forename: Ruslan
authors.initials: R
authors.lastname: Sadreyev
authors.forename: Jimin
authors.initials: J
authors.lastname: Pei
authors.forename: David
authors.initials: D
authors.lastname: Kim
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Kellogg
authors.forename: Frank
authors.initials: F
authors.lastname: DiMaio
authors.forename: Oliver
authors.initials: O
authors.lastname: Lange
authors.forename: Lisa
authors.initials: L
authors.lastname: Kinch
authors.forename: Will
authors.initials: W
authors.lastname: Sheffler
authors.forename: Bong-Hyun
authors.initials: BH
authors.lastname: Kim
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
references.citation: Protein Sci. 2007 Feb;16(2):165-75
references.pmid: 17189483
references.citation: Bioinformatics. 2005 Apr 1;21(7):951-60
references.pmid: 15531603
references.citation: Proteins. 2007;69 Suppl 8:118-28
references.pmid: 17894356
references.citation: Nucleic Acids Res. 2009 Jun;37(11):3522-30
references.pmid: 19357092
references.citation: Proc Natl Acad Sci U S A. 2004 May 4;101(18):6946-51
references.pmid: 15118103
references.citation: Annu Rev Biochem. 2008;77:363-82
references.pmid: 18410248
references.citation: Bioinformatics. 2008 Dec 1;24(23):2780-1
references.pmid: 18818215
references.citation: Nucleic Acids Res. 2006;34(16):4364-74
references.pmid: 16936316
references.citation: Proc Natl Acad Sci U S A. 1961 Sep 15;47:1309-14
references.pmid: 13683522
references.citation: Science. 2005 Sep 16;309(5742):1868-71
references.pmid: 16166519
references.citation: Proteins. 1999 May 1;35(2):133-52
references.pmid: 10223287
references.citation: Protein Sci. 2002 Aug;11(8):1937-44
references.pmid: 12142448
references.citation: Nat Protoc. 2009;4(1):1-13
references.pmid: 19131951
references.citation: Protein Sci. 2009 Jan;18(1):229-39
references.pmid: 19177366
references.citation: Protein Sci. 2003 May;12(5):963-72
references.pmid: 12717019
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Proteins. 2006 Dec 1;65(4):922-9
references.pmid: 17034045
references.citation: Proteins. 2007 Dec 1;69(4):758-63
references.pmid: 17671979
references.citation: Nature. 1992 Mar 19;356(6366):263-5
references.pmid: 1552947
references.citation: Nature. 2007 Nov 8;450(7167):259-64
references.pmid: 17934447
references.citation: Bioinformatics. 2003 May 22;19(8):1015-8
references.pmid: 12761065
references.citation: Methods Enzymol. 2004;383:66-93
references.pmid: 15063647
references.citation: Nat Methods. 2009 Aug;6(8):551-2
references.pmid: 19644455
references.citation: Nucleic Acids Res. 2006;34(17):e112
references.pmid: 16971460
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W653-8
references.pmid: 17517780
references.citation: Database (Oxford). 2009;2009:bap003
references.pmid: 20157476
references.citation: Nature. 2004 May 20;429(6989):318-322
references.pmid: 15152257
references.citation: Proteins. 2005;61 Suppl 7:128-34
references.pmid: 16187354
references.citation: Proteins. 1999;Suppl 3:22-9
references.pmid: 10526349
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Bioinformatics. 2007 Apr 1;23(7):802-8
references.pmid: 17267437
references.citation: J Mol Biol. 2003 Feb 7;326(1):317-36
references.pmid: 12547212
references.citation: Proteins. 2003;53 Suppl 6:542-7
references.pmid: 14579344