Systematic assessment of accuracy of comparative model of proteins belonging to different structural fold classes

Journal of Molecular Modeling

Volumn 17, Issue 11, 2011, Pages 2831-2837

  Chakravarty, Suvobrata ^a   Ghersi, Dario ^b,c   Sanchez, Roberto ^b  

^a SOUTH DAKOTA STATE UNIVERSITY   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

Alignment accuracy; Homology modeling; Information content; Model accuracy; Secondary structure; Sequence alignment

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; COMPARATIVE STUDY; ENTROPY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TARGETING; STRUCTURAL HOMOLOGY;

AMINO ACID SEQUENCE; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 80255140369     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-0976-9     Document Type: Article

References (48)

1. WR Taylor 2007 Evolutionary transitions in protein fold space Curr Opin Struct Biol 17 354 361 10.1016/j.sbi.2007.06.002 1:CAS:528:DC%2BD2sXnsFKks7Y%3D (Pubitemid 47021367)
2. Sanchez R, Sali A (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 95:13597-13602 (Pubitemid 28523017)
3. Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, Madhusudhan MS, Mirkovic N, Sali A (2000) Protein structure modeling for structural genomics. Nat Struct Biol 7(Suppl 1):986-990
4. RC Stevens S Yokoyama IA Wilson 2001 Global efforts in structural genomics Science 294 89 92 10.1126/science.1066011 1:CAS:528: DC%2BD3MXnsFyisbg%3D (Pubitemid 32952954)
5. A Tramontano V Morea 2003 Assessment of homology-based predictions in CASP5 Proteins 53 Suppl 6 352 368 10.1002/prot.10543 1:CAS:528: DC%2BD3sXptVygt7o%3D (Pubitemid 37352194)
6. GH Lushington 2008 Comparative modeling of proteins Meth Mol Biol Clifton NJ 443 199 212 1:CAS:528:DC%2BD1cXktFCju7k%3D
7. S Chakravarty L Wang R Sanchez 2005 Accuracy of structure-derived properties in simple comparative models of protein structures Nucleic Acids Res 33 244 259 10.1093/nar/gki162 1:CAS:528:DC%2BD2MXmsVygsA%3D%3D (Pubitemid 40276946)
8. S Chakravarty R Sanchez 2004 Systematic analysis of added-value in simple comparative models of protein structure Struct Camb 12 1461 1470 1:CAS:528:DC%2BD2cXmsVKntLw%3D (Pubitemid 39092090)
9. C Kiel S Wohlgemuth F Rousseau J Schymkowitz J Ferkinghoff-Borg F Wittinghofer L Serrano 2005 Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations J Mol Biol 348 759 775 10.1016/j.jmb.2005.02.046 1:CAS:528:DC%2BD2MXjt1Wjtrc%3D (Pubitemid 40515681)
10. T Liu A Rojas Y Ye A Godzik 2003 Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family Protein Sci 12 1872 1881 10.1110/ps.0359603 1:CAS:528:DC%2BD3sXmvVehsr0%3D (Pubitemid 37022810)
11. PS Murray Z Li J Wang CL Tang B Honig D Murray 2005 Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle Structure 13 1521 1531 10.1016/j.str.2005.07.010 1:CAS:528:DC%2BD2MXhtFWhtr3N (Pubitemid 41427591)
12. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C (2002) The Protein Data Bank. Acta Crystallogr D 58:899-907 (Pubitemid 34653017)
13. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242 (Pubitemid 30047768)
14. A Hillisch LF Pineda R Hilgenfeld 2004 Utility of homology models in the drug discovery process Drug Discov Today 9 659 669 10.1016/S1359-6446(04)03196-4 1:CAS:528:DC%2BD2cXmtVSktb0%3D (Pubitemid 38981720)
15. CS Ring E Sun JH McKerrow GK Lee PJ Rosenthal ID Kuntz FE Cohen 1993 Structure-based inhibitor design by using protein models for the development of antiparasitic agents Proc Natl Acad Sci USA 90 3583 3587 10.1073/pnas.90.8.3583 1:CAS:528:DyaK3sXktVShu7o%3D (Pubitemid 23111411)
16. A Evers T Klabunde 2005 Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor J Med Chem 48 1088 1097 10.1021/jm0491804 1:CAS:528:DC%2BD2MXptlSmsg%3D%3D (Pubitemid 40270452)
17. A Evers G Klebe 2004 Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model J Med Chem 47 5381 5392 10.1021/jm0311487 1:CAS:528:DC%2BD2cXnvFSrsLo%3D (Pubitemid 39382788)
18. E Vangrevelinghe K Zimmermann J Schoepfer R Portmann D Fabbro P Furet 2003 Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking J Med Chem 46 2656 2662 10.1021/jm030827e 1:CAS:528:DC%2BD3sXjvVGmsbY%3D (Pubitemid 36702534)
19. T Lengauer C Lemmen M Rarey M Zimmermann 2004 Novel technologies for virtual screening Drug Discov Today 9 27 34 10.1016/S1359-6446(04)02939-3 1:CAS:528:DC%2BD2cXhtVOjur0%3D (Pubitemid 38169029)
20. Read RJ (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D 57(Pt 10):1373-1382 (Pubitemid 36117185)
21. J Skolnick JS Fetrow A Kolinski 2000 Structural genomics and its importance for gene function analysis Nat Biotech 18 283 287 10.1038/73723 1:CAS:528:DC%2BD3cXhvVyrur4%3D (Pubitemid 30159478)
22. J Moult 2005 A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction Curr Opin Struct Biol 15 285 289 10.1016/j.sbi.2005.05.011 1:CAS:528:DC%2BD2MXlt1SrsLw%3D (Pubitemid 40826447)
23. S Chakravarty S Godbole B Zhang S Berger R Sanchez 2008 Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure BMC Struct Biol 8 31 10.1186/1472-6807-8-31
24. JM Sauder JW Arthur RL Dunbrack Jr 2000 Large-scale comparison of protein sequence alignment algorithms with structure alignments Proteins 40 6 22 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7 1:CAS:528:DC%2BD3cXjvFyjur0%3D (Pubitemid 30368577)
25. RL Dunbrack Jr 2006 Sequence comparison and protein structure prediction Curr Opin Struct Biol 16 374 384 10.1016/j.sbi.2006.05.006 1:CAS:528: DC%2BD28Xls1aksLs%3D (Pubitemid 43831651)
26. D Baker A Sali 2001 Protein structure prediction and structural genomics Science 294 93 96 10.1126/science.1065659 1:CAS:528:DC%2BD3MXnsFyisbY%3D (Pubitemid 32952955)
27. J Kopp L Bordoli JN Battey F Kiefer T Schwede 2007 Assessment of CASP7 predictions for template-based modeling targets Proteins 69 Suppl 8 38 56 10.1002/prot.21753 1:CAS:528:DC%2BD2sXhsVSgt7bL (Pubitemid 350210112)
28. A Nayeem D Sitkoff S Krystek Jr 2006 A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models Protein Sci 15 808 824 10.1110/ps.051892906 1:CAS:528:DC%2BD28XjsFCqtrw%3D
29. A Rayan 2009 New tips for structure prediction by comparative modeling Bioinformation 3 263 267
30. A Sali TL Blundell 1993 Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 234 779 815 10.1006/jmbi.1993.1626 1:CAS:528:DyaK2cXnt1ylug%3D%3D (Pubitemid 24007801)
31. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D (Pubitemid 27359211)
32. L Rychlewski L Jaroszewski W Li A Godzik 2000 Comparison of sequence profiles. Strategies for structural predictions using sequence information Protein Sci 9 232 241 10.1110/ps.9.2.232 1:CAS:528:DC%2BD3cXhs12ku7c%3D (Pubitemid 30126996)
33. RI Sadreyev NV Grishin 2004 Estimates of statistical significance for comparison of individual positions in multiple sequence alignments BMC Bioinf 5 106 10.1186/1471-2105-5-106 (Pubitemid 40195400)
34. AR Panchenko 2003 Finding weak similarities between proteins by sequence profile comparison Nucleic Acids Res 31 683 689 10.1093/nar/gkg154 1:CAS:528:DC%2BD3sXitlCgu7Y%3D (Pubitemid 36175958)
35. Casbon J, Saqi MA (2005) S4: structure-based sequence alignments of SCOP superfamilies. Nucleic Acids Res 33:D219-222 (Pubitemid 40207864)
36. ML Tress D Jones A Valencia 2003 Predicting reliable regions in protein alignments from sequence profiles J Mol Biol 330 705 718 10.1016/S0022-2836(03) 00622-3 1:CAS:528:DC%2BD3sXlt1aqtL8%3D
37. RI Sadreyev NV Grishin 2004 Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs Bioinformatics 20 818 828 10.1093/bioinformatics/btg485 1:CAS:528:DC%2BD2cXjt1aqtLk%3D (Pubitemid 38559721)
38. P Koehl M Levitt 2002 Protein topology and stability define the space of allowed sequences Proc Natl Acad Sci USA 99 1280 1285 10.1073/pnas.032405199 1:CAS:528:DC%2BD38Xht1Cmu7s%3D (Pubitemid 34136484)
39. JL England EI Shakhnovich 2003 Structural determinant of protein designability Phys Rev Lett 90 218101 10.1103/PhysRevLett.90.218101
40. DL Minor Jr PS Kim 1994 Context is a major determinant of beta-sheet propensity Nature 371 264 267 10.1038/371264a0 1:CAS:528:DyaK2cXmvFGgtbY%3D (Pubitemid 24293028)
41. KF Han D Baker 1995 Recurring local sequence motifs in proteins J Mol Biol 251 176 187 10.1006/jmbi.1995.0424 1:CAS:528:DyaK2MXnsVCmsr8%3D
42. KF Han D Baker 1996 Global properties of the mapping between local amino acid sequence and local structure in proteins Proc Natl Acad Sci USA 93 5814 5818 10.1073/pnas.93.12.5814 1:CAS:528:DyaK28Xjs1Kqu7c%3D (Pubitemid 26190760)
43. Bystroff C, Simons KT, Han KF, Baker D (1996) Local sequence-structure correlations in proteins. Curr Opin Biotechnol 7:417-421 (Pubitemid 26265622)
44. MW West MH Hecht 1995 Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins Protein Sci 4 2032 2039 10.1002/pro.5560041008 1:CAS:528:DyaK2MXoslygtro%3D
45. BE Shakhnovich E Deeds C Delisi E Shakhnovich 2005 Protein structure and evolutionary history determine sequence space topology Genom Res 15 385 392 10.1101/gr.3133605 1:CAS:528:DC%2BD2MXitVWksLo%3D (Pubitemid 40467780)
46. RC Edgar K Sjolander 2004 A comparison of scoring functions for protein sequence profile alignment Bioinformatics 20 1301 1308 10.1093/bioinformatics/ bth090 1:CAS:528:DC%2BD2cXkt1Sruro%3D (Pubitemid 38807585)
47. V Anantharaman L Aravind EV Koonin 2003 Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins Curr Opin Chem Biol 7 12 20 10.1016/S1367-5931(02)00018-2 1:CAS:528: DC%2BD3sXltlaqsg%3D%3D (Pubitemid 36126487)
48. RC Edgar 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinf 5 113 10.1186/1471-2105-5-113 (Pubitemid 40195393)