Improved Scoring Function for Comparative Modeling Using the M4T Method

Overview

Journal J Struct Funct Genomics

Specialty Genetics

Date 2008 Nov 6

PMID 18985440

Citations 17

Authors

Dmitry Rykunov

Elliot Steinberger

Carlos J Madrid-Aliste

Andras Fiser

Affiliations

Soon will be listed here.

Abstract

Improvements in comparative protein structure modeling for the remote target-template sequence similarity cases are possible through the optimal combination of multiple template structures and by improving the quality of target-template alignment. Recently developed MMM and M4T methods were designed to address these problems. Here we describe new developments in both the alignment generation and the template selection parts of the modeling algorithms. We set up a new scoring function in MMM to deliver more accurate target-template alignments. This was achieved by developing and incorporating into the composite scoring function a novel statistical pairwise potential that combines local and non-local terms. The non-local term of the statistical potential utilizes a shuffled reference state definition that helped to eliminate most of the false positive signal from the background distribution of pairwise contacts. The accuracy of the scoring function was further increased by using BLOSUM mutation table scores.

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References

Shi J, Blundell T, Mizuguchi K . FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol. 2001; 310(1):243-57. DOI: 10.1006/jmbi.2001.4762. View

Fernandez-Fuentes N, Rai B, Madrid-Aliste C, Fajardo J, Fiser A . Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics. 2007; 23(19):2558-65. DOI: 10.1093/bioinformatics/btm377. View

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

Greer J . Comparative model-building of the mammalian serine proteases. J Mol Biol. 1981; 153(4):1027-42. DOI: 10.1016/0022-2836(81)90465-4. View

Chothia C, Lesk A, Levitt M, Amit A, Mariuzza R, Phillips S . The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science. 1986; 233(4765):755-8. DOI: 10.1126/science.3090684. View

Sutcliffe M, Haneef I, Carney D, Blundell T . Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1987; 1(5):377-84. DOI: 10.1093/protein/1.5.377. View

Levitt M . Accurate modeling of protein conformation by automatic segment matching. J Mol Biol. 1992; 226(2):507-33. DOI: 10.1016/0022-2836(92)90964-l. View

Russell R, Barton G . Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins. 1992; 14(2):309-23. DOI: 10.1002/prot.340140216. View

Henikoff S, Henikoff J . Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992; 89(22):10915-9. PMC: 50453. DOI: 10.1073/pnas.89.22.10915. View

10.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

11.

Miyazawa S, Jernigan R . Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol. 1996; 256(3):623-44. DOI: 10.1006/jmbi.1996.0114. View

12.

Cardozo T, Totrov M, Abagyan R . Homology modeling by the ICM method. Proteins. 1995; 23(3):403-14. DOI: 10.1002/prot.340230314. View

13.

Rice D, Eisenberg D . A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol. 1997; 267(4):1026-38. DOI: 10.1006/jmbi.1997.0924. View

14.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

15.

Sanchez R, Sali A . Evaluation of comparative protein structure modeling by MODELLER-3. Proteins. 1997; Suppl 1:50-8. DOI: 10.1002/(sici)1097-0134(1997)1+<50::aid-prot8>3.3.co;2-w. View

16.

Sanchez R, Sali A . Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A. 1998; 95(23):13597-602. PMC: 24864. DOI: 10.1073/pnas.95.23.13597. View

17.

Burley S, Almo S, Bonanno J, Capel M, Chance M, Gaasterland T . Structural genomics: beyond the human genome project. Nat Genet. 1999; 23(2):151-7. DOI: 10.1038/13783. View

18.

Yang A, Honig B . Sequence to structure alignment in comparative modeling using PrISM. Proteins. 1999; Suppl 3:66-72. DOI: 10.1002/(sici)1097-0134(1999)37:3+<66::aid-prot10>3.3.co;2-b. View

19.

Fiser A . Protein structure modeling in the proteomics era. Expert Rev Proteomics. 2005; 1(1):97-110. DOI: 10.1586/14789450.1.1.97. View

20.

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