Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Bioinformatics

Volumn 28, Issue 14, 2012, Pages 1851-1857

  Buenavista, Maria T ^a,b,c   Roche, Daniel B ^a   McGuffin, Liam J ^a  

^a UNIVERSITY OF READING   (United Kingdom)

^b MRC Harwell   (United Kingdom)

^c DIAMOND LIGHT SOURCE LTD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; METHODOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT;

EID: 84864125649     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts292     Document Type: Article

References (37)

1. Chakravarty, S. et al. (2008) Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure. BMC. Struct. Biol., 8, 31.
2. Cheng, J. (2008) A multi-template combination algorithm for protein comparative modeling. BMC Struct. Biol., 8, 18.
3. Chubb, D. et al. (2010) Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe. Bioinformatics, 26, 2664-2671.
4. Contreras-Moreira, B. et al. (2003) In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J. Mol. Biol., 328, 593-608.
5. Fischer, D. (2003) 3D-SHOTGUN: a novel, cooperative, fold-recognition metapredictor. Proteins, 51, 434-441.
6. Fiser, A. and Sali, A. (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol., 374, 361-491.
7. Ginalski, K. et al. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
8. Hildebrand, A. et al. (2009) Fast and accurate automatic structure prediction with HHpred. Proteins, 77, 128-132.
9. Kryshtafovych, A. et al. (2011) Evaluation of model quality predictions in CASP9. Proteins, 79, 91-106.
10. Larsson, P. et al. (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Prot. Sci., 17, 990-1002.
11. Larsson, P. et al. (2011) Improved predictions by Pcons. net using multiple templates. Bioinfromatics., 27, 426-427.
12. Liu, T. et al. (2008) Improving the accuracy of template-based predictions by mixing and matching between initial models. BMC Struct. Biol., 8, 24.
13. Lundstrom, J. et al. (2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Prot. Sci., 10, 2354-2362.
14. Mariani, V. et al. (2011) Assessment of template based protein structure predictions in CASP9. Proteins, 79, 37-58.
15. Martínez, L. et al. (2007) Convergent algorithms for protein structural alignment. BMC Bioinformatics, 8, 306.
16. McGuffin, L. J. (2010) Model quality prediction. In: Rangwala, H. and Karypis, G. (eds.) Introduction to Protein Structure Prediction: Methods and Algorithms. Wiley, New Jersey, pp. 323-342.
17. McGuffin, L. J. and Roche, D. B. (2009) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics, 26, 182-188.
18. McGuffin, L. J. and Roche, D. B. (2011) Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method. Prot.: Struct. Funct. Bioinformatics, 79, 137-146.
19. Peng, J. and Xu, J. (2011a) A multiple-template approach to protein threading. Prot.: Struct. Funct. Bioinformatics, 79, 1930-1939.
20. Peng, J. and Xu, J. (2011b) Raptorx: exploiting structure information for protein alignment by statistical inference. Prot.: Struct. Funct. Bioinformatics, 79, 161-171.
21. Roche, D. B. et al. (2011) The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. Nucleic Acids Res., 39, W171-W176.
22. Roy, A. et al. (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc., 5, 725-738.
23. Siew, N. et al. (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16, 776-785.
24. Soding, J. (2004) Protein homology detection by HMM-HMM comparison, Bioinformatics, 21, 951-960.
25. Soding, J. et al. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
26. Tramontano, A. and Cozzetto, D. (2011) Evaluation of protein structure prediction methods: issues and strategies. In: Kolinski, A. (ed.). Multi-scale Approaches to Protein Modelling. Springer, New York, pp. 315-339.
27. Tramontano, A. et al. (2008) The assessment of methods for protein structure prediction. In: Zaki, M. and Bystroff, C. (eds.). Protein Structure Prediction. Humana Press, New Jersey, pp. 43-57.
28. Wallner, B. and Elofsson, A. (2003) Can correct protein models be identified? Protein Sci., 12, 1073-1086.
29. Wallner, B. et al. (2007) Pcons. net: protein structure prediction meta server. Nucleic Acids Res., 35, W369-W374.
30. Wang, Z. et al. (2010) MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics, 26, 882-888.
31. Wang, Z. et al. (2011) APOLLO: a quality assessment service for single and multiple protein models. Bioinformatics, 27, 1715-1716.
32. Wu, S. and Zhang, Y. (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res., 35, 3375-3382.
33. Xu, J. and Zhang, Y. (2010) How significant is a protein structure similarity with TMscore = 0. 5? Bioinformatics, 26, 889-895.
34. Zemla, A. et al. (2001) Processing and evaluation of predictions in CASP4. Proteins, 45, 13-21.
35. Zhang, Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40.
36. Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
37. Zhou, H. and Zhou, Y. (2005) SPARKS 2 and SP3 servers in CASP6. Proteins, 61, 152-156.