Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue SUPPL. 10, 2011, Pages 147-160

  Xu, Dong ^a   Zhang, Jian ^a   Roy, Ambrish ^a   Zhang, Yang ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

ab initio folding; CASP; Contact prediction; Protein structure prediction; Threading

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; ANALYTIC METHOD; ARTICLE; FRAGMENT GUIDED MOLECULAR DYNAMIC; HYDROGEN BOND; I TASSER; MOLECULAR DYNAMICS; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTEIN TARGETING; QUARK;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MOLECULAR DYNAMICS SIMULATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE;

EID: 80855147432     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23111     Document Type: Article

References (56)

1. Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007; 69 (Suppl 8): 38-56.
2. Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins 2009; 77 (Suppl 9): 18-28.
3. Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol 2008; 18: 342-348.
4. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005; 21: 951-960.
5. Wu S, Zhang Y. MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 2008; 72: 547-556.
6. Peng J, Xu J. Boosting protein threading accuracy. Lect Notes Comput Sci 2009; 5541: 31.
7. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 2007; 35: 3375-3382.
8. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003; 19: 1015-1018.
9. Cheng J. A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol 2008; 8: 18.
10. Zhang J, Wang Q, Barz B, He Z, Kosztin I, Shang Y, Xu D. MUFOLD: a new solution for protein 3D structure prediction. Proteins 2010; 78: 1137-1152.
11. Floudas CA. Computational methods in protein structure prediction. Biotechnol Bioeng 2007; 97: 207-213.
12. Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003; 51: 434-441.
13. Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007; 69 (Suppl 8): 108-117.
14. Arakaki AK, Zhang Y, Skolnick J. Large scale assesment of the utility of low resolution protein structures for biochemical function assignment. Bioinformatics 2004; 20: 1087-1096.
15. Zhang Y. Protein structure prediction: when is it useful?. Curr Opin Struct Biol 2009; 19: 145-155.
16. Jauch R, Yeo HC, Kolatkar PR, Clarke ND. Assessment of CASP7 structure predictions for template free targets. Proteins 2007; 69 (Suppl 8): 57-67.
17. Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y. Assessment of CASP8 structure predictions for template free targets. Proteins 2009; 77 (Suppl 9): 50-65.
18. Floudas CA, Fung HK, McAllister SR, Monnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: a review. Chem Eng Sci 2006; 61: 966-988.
19. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
20. Bowie JU, Eisenberg D. An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 1994; 91: 4436-4440.
21. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
22. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010; 5: 725-738.
23. Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007; 5: 17.
24. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008; 9: 40.
25. Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009; 77 (Suppl 9): 100-113.
26. Li Y, Zhang Y. REMO: a new protocol to refine full atomic protein models from C-α traces by optimizing hydrogen-bonding networks. Proteins 2009; 76: 665-676.
27. Zhang J, Liang Y, Zhang Y. Atomic-level protein structure refinement using fragment guided molecular dynamics conformation sampling. Submitted, 2011.
28. Xu D, Zhang Y. Ab initio protein structure prediction using QUARK: I. method design and validation. Submitted, 2011.
29. Xu D, Zhang Y. Ab initio protein structure prediction using QUARK: II. algorithm flow and benchmark result. Submitted, 2011.
30. Shi J, Blundell TL, Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001; 310: 243-257.
31. Xu Y, Xu D. Protein threading using PROSPECT: design and evaluation. Proteins 2000; 40: 343-354.
32. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003; 53 (Suppl 6): 491-496.
33. Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004; 55: 1005-1013.
34. Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005; 58: 321-328.
35. Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 2005; 102: 1029-1034.
36. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004; 101: 7594-7599.
37. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003; 85: 1145-1164.
38. Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci USA 2006; 103: 2605-2610.
39. Chen H, Zhou HX. Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res 2005; 33: 3193-3199.
40. Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 2008; 24: 924-931.
41. Wu S, Szilagyi A, Zhang Y. Improving protein structure prediction using multiple sequence-based contact predictions. 2010 Structure, in press (2011).
42. Wu S, Zhang Y. Recognizing protein substructure similarity using segmental threading. Structure 2010; 18: 858-867.
43. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004; 25: 865-871.
44. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005; 33: 2302-2309.
45. Plimpton S. Fast parallel algorithms for short-range molecular dynamics. J Comput Phys 1995; 117: 1-19.
46. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KMJ, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995; 117: 5179-5197.
47. Xu D, Zhang Y. What is optimum fragment length for ab initio protein structure assembly? Submitted, 2011.
48. Holm L, Sander C. Database algorithm for generating protein backbone and side-chain co-ordinates from a C α trace application to model building and detection of co-ordinate errors. J Mol Biol 1991; 218: 183-194.
49. Levy-Moonshine A, Amir el AD, Keasar C. Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential. Bioinformatics 2009; 25: 2639-2645.
50. Rotkiewicz P, Skolnick J. Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem 2008; 29: 1460-1465.
51. McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994; 238: 777-793.
52. Li Y, Roy A, Zhang Y. HAAD: a quick algorithm for accurate prediction of hydrogen atoms in protein structures. PLo S One 2009; 4: e6701.
53. Chen VB, Arendall WBIII, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 2010; 66 (Part 1): 12-21.
54. Cheng J, Baldi P. Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005; 21 (Suppl 1): i75-i84.
55. Klepeis JL, Floudas CA. ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J 2003; 85: 2119-2146.
56. Rajgaria R, Wei Y, Floudas CA. Contact prediction for α and α-β proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD. Proteins 2010; 78: 1825-1846.