Detection of homologous proteins by an intermediate sequence search

Protein Science

Volumn 13, Issue 1, 2004, Pages 54-62

  John, Bino ^a   Sali, Andrej ^b  

^a ROCKEFELLER UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Comparative protein structure modeling; Fold assignment; Protein evolution; Protein homology; Sequence alignment

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; HUMAN; INTERMEDIATE SEQUENCE SEARCH; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTERS; DATABASES, FACTUAL; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0346734106     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03335004     Document Type: Article

References (40)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Apostolico, A. and Giancarlo, R. 1998. Sequence alignment in molecular biology. J. Comput. Biol. 5: 173-196.
4. Barton, G.J. 1994. Scop: Structural classification of proteins. Trends Biochem. Sci. 19: 554-555.
5. Blake, J.D. and Cohen, F.E. 2001. Pairwise sequence alignment below the twilight zone. J. Mol. Biol. 307: 721-735.
6. Brenner, S.E., Koehl, P., and Levitt, M. 2000. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res. 28: 254-256.
7. Burley, S.K. and Bonanno, J.B. 2003. Structural genomics. Methods Biochem. Anal. 44: 591-612.
8. Burley, S.K., Almo, S.C., Bonanno, J.B., Capel, M., Chance, M.R., Gaasterland, T., Lin, D., Sali, A., Studier, F.W., and Swaminathan, S. 1999. Structural genomics: Beyond the human genome project. Nat. Genet. 23: 151-157.
9. Cantor, C.R. and Little, D.P. 1998. Massive attack on high-throughput biology. Nat. Genet. 20: 5-6.
10. Contreras-Moreira, B., Fitzjohn, P.W., and Bates, P.A. 2003. In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling. J. Mol. Biol. 328: 593-608.
11. Gerstein, M. 1998. Measurement of the effectiveness of transitive sequence comparison, through a third "intermediate" sequence. Bioinformatics 14: 707-714.
12. Gerstein, M. and Levitt, M. 1998. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci. 7: 445-456.
13. Goodrich, M.T. and Tamassia, R. 2002. Algorithm design foundations, analysis, and internet examples. Wiley, New York.
14. Grunenfelder, B. and Winzeler, E.A. 2002. Treasures and traps in genome-wide data sets: Case examples from yeast. Nat. Rev. Genet. 3: 653-661.
15. Guenther, B., Onrust, R., Sali, A., O'Donnell, M., and Kuriyan, J. 1997. Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91: 335-345.
16. Henikoff, S. and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915-10919.
17. John, B. and Sali, A. 2003. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 31: 3982-3992.
18. Kann, M., Qian, B., and Goldstein, R.A. 2000. Optimization of a new score function for the detection of remote homologs. Proteins 41: 498-503.
19. Li, W., Pio, F., Pawlowski, K., and Godzik, A. 2000. Saturated BLAST: An automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 16: 1105-1110.
20. Li, W., Jaroszewski, L., and Godzik, A. 2002. Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 15: 643-649.
21. Lo, C.L., Ailey, B., Hubbard, T.J., Brenner, S.E., Murzin, A.G., and Chothia, C. 2000. SCOP: A structural classification of proteins database. Nucleic Acids Res. 28: 257-259.
22. Park, J., Teichmann, S.A., Hubbard, T., and Chothia, C. 1997. Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol. 273: 349-354.
23. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T., and Chothia, C. 1998. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284: 1201-1210.
24. Pearson, W.R. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183: 63-98.
25. Pennisi, E. 2003. Human genome. A low number wins the GeneSweep Pool. Science 300: 1484.
26. Pieper, U., Eswar, N., Ilyin, V.A., Stuart, A., and Sali, A. 2002. ModBase, a database of annotated comparative protein structure models. Nucleic Acids Res. 30: 255-259.
27. Pipenbacher, P., Schliep, A., Schneckener, S., Schonhuth, A., Schomburg, D., and Schrader, R. 2002. ProClust: Improved clustering of protein sequences with an extended graph-based approach. Bioinformatics 2: 182-191.
28. Salamov, A.A., Suwa, M., Orengo, C.A., and Swindells, M.B. 1999. Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng. 12: 95-100.
29. Sali, A. 1998. 100,000 protein structures for the biologist. Nat. Struct. Biol. 5: 1029-1032.
30. Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
31. Sanchez, R. and Sali, A. 1997. Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol 7: 206-214.
32. - 1998. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. 95: 13597-13602.
33. - 2000. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol. Biol. 143: 97-129.
34. Saqi, M.A., Bates, P.A., and Sternberg, M.J. 1992. Towards an automatic method of predicting protein structure by homology: An evaluation of suboptimal sequence alignments. Protein Eng. 5: 305-311.
35. Serres, M.H., Gopal, S., Nahum, L.A., Liang, P., Gaasterland, T., and Riley, M. 2001. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2: RESEARCH0035.
36. Sippl, M.J., Lackner, P., Domingues, F.S., Prlic, A., Malik, R., Andreeva, A., and Wiederstein, M. 2001. Assessment of the CASP4 fold recognition category. Proteins 5: 55-67.
37. Teichmann, S.A., Chothia, C., Church, G.M., and Park, J. 2000. Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics 16: 117-124.
38. Terwilliger, T.C. 2000. Structural genomics in North America. Nat. Struct. Biol. 7: 935-939.
39. Theodoridis, S. and Koutroumbos, K. 1999. Pattern recognition, pp. 149-150. Academic Press, San Diego, CA.
40. Vitkup, D., Melamud, E., Moult, J., and Sander, C. 2001. Completeness in structural genomics. Nat. Struct. Biol. 8: 559-566.