On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5724 LNBI, Issue , 2009, Pages 62-72

  Di Lena, Pietro ^a   Fariselli, Piero ^a   Margara, Luciano ^a   Vassura, Marco ^a   Casadio, Rita ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EQUIVALENT MATRICES; LINEAR CORRELATION; OPTIMIZATION PROCEDURES; PEARSON COEFFICIENT; PEARSON CORRELATION COEFFICIENTS; PREDICTION ACCURACY; PROTEIN RESIDUES; SIMILARITY MATRIX; THREE-DIMENSIONAL STRUCTURE; UPPER BOUND; UPPER LIMITS;

BIOINFORMATICS; PROTEIN FOLDING;

MATRIX ALGEBRA;

EID: 70350417738     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04241-6_6     Document Type: Conference Paper

References (18)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389-3402 (1997)
2. Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C., Murzin, A.G.: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32(Database issue), D226-D229 (2004)
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Res. 28(1), 235-242 (2000)
4. Das, R., Baker, D.: Macromolecular modeling with rosetta. Annu. Rev. Biochem. 77, 363-382 (2008)
5. Göbel, U., Sander, C., Schneider, R., Valencia, A.: Correlated mutations and residue contacts in proteins. Proteins 18(4), 309-317 (1994)
6. Graña, O., Eyrich, V.A., Pazos, F., Rost, B., Valencia, A.: EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res. 33(Web Server issue), W347-W351 (2005)
7. Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U S A 89(22), 10915-10919 (1992)
8. Horner, D.S., Pirovano, W., Pesole, G.: Correlated substitution analysis and the prediction of amino acid structural contacts. Brief Bioinform. 9(1), 46-56 (2008); Epub. (November 13, 2007)
9. Izarzugaza, J.M., Graña, O., Tress, M.L., Valencia, A., Clarke, N.D.: Assessment of intramolecular contact predictions for CASP7. Proteins 69(suppl. 8), 152-158 (2007)
10. Hinds, D.A., Levitt, M.: A lattice model for protein structure prediction at low resolution. Proc. Natl. Acad. Sci. U S A 89(7), 2536-2540 (1992)
11. Lesk, A.: Introduction to Bioinformatics. Oxford University Press, Oxford (2006)
12. McLachlan, A.D.: Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551. J. Mol. Biol. 61(2), 409-424 (1971)
13. Olmea, O., Valencia, A.: Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des. 2(3), S25-S32 (1997)
14. Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.: A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure 5(3), 345-352 (1978); Dayhoff, M.O. (ed.)
15. Pollock, D.D., Taylor, W.R.: Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10(6), 647-657 (1997)
16. Samsonov, S.A., Teyra, J., Anders, G., Pisabarro, M.T.: Analysis of the impact of solvent on contacts prediction in proteins. BMC Struct. Biol. 9(1), 22 (2009)
17. Snyman, J.A.: Practical mathematical optimization: an introduction to basic optimization theory and classical and new gradient-based algorithms. Springer, New York (2005)
18. Vassura, M., Margara, L., Di Lena, P., Medri, F., Fariselli, P., Casadio, R.: Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans. Comput. Biol. Bioinform. 5(3), 357-367 (2008)