title: Improving threading algorithms for remote homology modeling by combining fragment and template comparisons.
abstract: In this work, we develop a method called fragment comparison and the template comparison (FTCOM) for assessing the global quality of protein structural models for targets of medium and hard difficulty (remote homology) produced by structure prediction approaches such as threading or ab initio structure prediction. FTCOM requires the C(alpha) coordinates of full length models and assesses model quality based on fragment comparison and a score derived from comparison of the model to top threading templates. On a set of 361 medium/hard targets, FTCOM was applied to and assessed for its ability to improve on the results from the SP(3), SPARKS, PROSPECTOR_3, and PRO-SP(3)-TASSER threading algorithms. The average TM-score improves by 5-10% for the first selected model by the new method over models obtained by the original selection procedure in the respective threading methods. Moreover, the number of foldable targets (TM-score >or= 0.4) increases from least 7.6% for SP(3) to 54% for SPARKS. Thus, FTCOM is a promising approach to template selection. Proteins 2010. (c) 2010 Wiley-Liss, Inc.
authors.affiliation: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA.
authors.forename: Hongyi
authors.initials: H
authors.lastname: Zhou
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Skolnick
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D015233:Models, Statistical; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins
references.citation: Proc Natl Acad Sci U S A. 2004 May 18;101(20):7594-9
references.pmid: 15126668
references.citation: Proteins. 2007;69 Suppl 8:38-56
references.pmid: 17894352
references.citation: Nat Biotechnol. 2000 Mar;18(3):283-7
references.pmid: 10700142
references.citation: Bioinformatics. 2003 May 22;19(8):1015-8
references.pmid: 12761065
references.citation: Proteins. 2004 Aug 15;56(3):502-18
references.pmid: 15229883
references.citation: Protein Sci. 2001 Nov;10(11):2354-62
references.pmid: 11604541
references.citation: J Mol Biol. 2001 Mar 9;306(5):1191-9
references.pmid: 11237627
references.citation: Proteins. 2003;53 Suppl 6:534-41
references.pmid: 14579343
references.citation: Proteins. 2003 May 15;51(3):434-41
references.pmid: 12696054
references.citation: Proteins. 2009;77 Suppl 9:181-4
references.pmid: 19544564
references.citation: J Mol Biol. 1999 Apr 9;287(4):797-815
references.pmid: 10191147
references.citation: Proteins. 2008 May 15;71(3):1211-8
references.pmid: 18004783
references.citation: Bioinformatics. 2008 Feb 15;24(4):586-7
references.pmid: 18184684
references.citation: J Mol Biol. 1993 Dec 5;234(3):779-815
references.pmid: 8254673
references.citation: Protein Sci. 2006 Jul;15(7):1653-66
references.pmid: 16751606
references.citation: Proteins. 2009;77 Suppl 9:123-7
references.pmid: 19639638
references.citation: Proteins. 2007;69 Suppl 8:90-7
references.pmid: 17705276
references.citation: Methods Biochem Anal. 2003;44:525-46
references.pmid: 12647403
references.citation: Proteins. 2004 Jun 1;55(4):1005-13
references.pmid: 15146497
references.citation: Proteins. 2004 Dec 1;57(4):702-10
references.pmid: 15476259
references.citation: Bioinformatics. 2006 Jun 15;22(12):1456-63
references.pmid: 16547073
references.citation: Proteins. 2005;61 Suppl 7:91-8
references.pmid: 16187349
references.citation: IEEE/ACM Trans Comput Biol Bioinform. 2005 Apr-Jun;2(2):157-65
references.pmid: 17044180
references.citation: Proteins. 2009 May 15;75(3):638-47
references.pmid: 19004001
references.citation: Proteins. 2005;61 Suppl 7:152-6
references.pmid: 16187357
references.citation: Proteins. 2005 Feb 1;58(2):321-8
references.pmid: 15523666
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5361-6
references.pmid: 16567638
references.citation: Bioinformatics. 1998;14(10):846-56
references.pmid: 9927713
references.citation: Proteins. 2009 May 15;75(3):540-9
references.pmid: 19003987
references.citation: J Comput Chem. 2004 Apr 30;25(6):865-71
references.pmid: 15011258
references.citation: J Bioinform Comput Biol. 2003 Apr;1(1):95-117
references.pmid: 15290783
references.citation: Protein Sci. 2006 Apr;15(4):900-13
references.pmid: 16522791
references.citation: Science. 2001 Oct 5;294(5540):93-6
references.pmid: 11588250
references.citation: Proteins. 2005;61 Suppl 7:46-66
references.pmid: 16187346
references.citation: Proteins. 2008 Apr;71(1):261-77
references.pmid: 17932912
references.citation: Biophys J. 2007 Sep 1;93(5):1510-8
references.pmid: 17496016
references.citation: Biophys J. 2009 Mar 18;96(6):2119-27
references.pmid: 19289038
references.citation: Nucleic Acids Res. 2005 Apr 22;33(7):2302-9
references.pmid: 15849316
references.citation: J Mol Biol. 1997 Apr 25;268(1):209-25
references.pmid: 9149153