A Multi-template Combination Algorithm for Protein Comparative Modeling

Overview

Journal BMC Struct Biol

Publisher Biomed Central

Specialties Biochemistry
Molecular Biology

Date 2008 Mar 28

PMID 18366648

Citations 50

Authors

Jianlin Cheng

Affiliations

Soon will be listed here.

Abstract

Background: Multiple protein templates are commonly used in manual protein structure prediction. However, few automated algorithms of selecting and combining multiple templates are available.

Results: Here we develop an effective multi-template combination algorithm for protein comparative modeling. The algorithm selects templates according to the similarity significance of the alignments between template and target proteins. It combines the whole template-target alignments whose similarity significance score is close to that of the top template-target alignment within a threshold, whereas it only takes alignment fragments from a less similar template-target alignment that align with a sizable uncovered region of the target. We compare the algorithm with the traditional method of using a single top template on the 45 comparative modeling targets (i.e. easy template-based modeling targets) used in the seventh edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7). The multi-template combination algorithm improves the GDT-TS scores of predicted models by 6.8% on average. The statistical analysis shows that the improvement is significant (p-value < 10-4). Compared with the ideal approach that always uses the best template, the multi-template approach yields only slightly better performance. During the CASP7 experiment, the preliminary implementation of the multi-template combination algorithm (FOLDpro) was ranked second among 67 servers in the category of high-accuracy structure prediction in terms of GDT-TS measure.

Conclusion: We have developed a novel multi-template algorithm to improve protein comparative modeling.

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References

Tress M, Ezkurdia I, Grana O, Lopez G, Valencia A . Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins. 2005; 61 Suppl 7:27-45. DOI: 10.1002/prot.20720. View

Zhou H, Zhou Y . Quantifying the effect of burial of amino acid residues on protein stability. Proteins. 2003; 54(2):315-22. DOI: 10.1002/prot.10584. View

Westbrook J, Feng Z, Chen L, Yang H, Berman H . The Protein Data Bank and structural genomics. Nucleic Acids Res. 2003; 31(1):489-91. PMC: 165515. DOI: 10.1093/nar/gkg068. View

Sadreyev R, Grishin N . COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol. 2003; 326(1):317-36. DOI: 10.1016/s0022-2836(02)01371-2. View

Zhang Y, Skolnick J . Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A. 2004; 101(20):7594-9. PMC: 419651. DOI: 10.1073/pnas.0305695101. View

Schwede T, Diemand A, Guex N, Peitsch M . Protein structure computing in the genomic era. Res Microbiol. 2000; 151(2):107-12. DOI: 10.1016/s0923-2508(00)00121-2. View

Petrey D, Honig B . Protein structure prediction: inroads to biology. Mol Cell. 2005; 20(6):811-9. DOI: 10.1016/j.molcel.2005.12.005. View

Soding J . Protein homology detection by HMM-HMM comparison. Bioinformatics. 2004; 21(7):951-60. DOI: 10.1093/bioinformatics/bti125. View

Zhang Y . Template-based modeling and free modeling by I-TASSER in CASP7. Proteins. 2007; 69 Suppl 8:108-17. DOI: 10.1002/prot.21702. View

10.

Marti-Renom M, Madhusudhan M, Sali A . Alignment of protein sequences by their profiles. Protein Sci. 2004; 13(4):1071-87. PMC: 2280052. DOI: 10.1110/ps.03379804. View

11.

Mittelman D, Sadreyev R, Grishin N . Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics. 2003; 19(12):1531-9. DOI: 10.1093/bioinformatics/btg185. View

12.

Venclovas C, Margelevicius M . Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. Proteins. 2005; 61 Suppl 7:99-105. DOI: 10.1002/prot.20725. View

13.

Kim D, Chivian D, Baker D . Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004; 32(Web Server issue):W526-31. PMC: 441606. DOI: 10.1093/nar/gkh468. View

14.

Bates P, Kelley L, MacCallum R, STERNBERG M . Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins. 2002; Suppl 5:39-46. DOI: 10.1002/prot.1168. View

15.

Lambert C, Leonard N, De Bolle X, Depiereux E . ESyPred3D: Prediction of proteins 3D structures. Bioinformatics. 2002; 18(9):1250-6. DOI: 10.1093/bioinformatics/18.9.1250. View

16.

Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P . Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 2007; 69 Suppl 8:118-28. DOI: 10.1002/prot.21636. View

17.

Read R, Chavali G . Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins. 2007; 69 Suppl 8:27-37. DOI: 10.1002/prot.21662. View

18.

Stuart A, Fiser A, Sanchez R, Melo F, Sali A . Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000; 29:291-325. DOI: 10.1146/annurev.biophys.29.1.291. View

19.

Joo K, Lee J, Lee S, Seo J, Lee S, Lee J . High accuracy template based modeling by global optimization. Proteins. 2007; 69 Suppl 8:83-9. DOI: 10.1002/prot.21628. View

20.

Guex N, Peitsch M . SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1998; 18(15):2714-23. DOI: 10.1002/elps.1150181505. View