Comparison of sequence profiles. Strategies for structural predictions using sequence information

Protein Science

Volumn 9, Issue 2, 2000, Pages 232-241

  Rychlewski, Leszek ^a   Jaroszewski, Lukasz ^b   Li, Weizhong ^a   Godzik, Adam ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BURNHAM INSTITUTE   (United States)

Author keywords

Fold recognition; PSI BLAST; Sequence profile

Indexed keywords

AMINO ACID; CYTOKINE;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; GENOME; INFORMATION SYSTEM; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0033997036     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.2.232     Document Type: Article

References (25)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3):403-410.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402.
3. Aravind L, Koonin EV. 1999. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 287(5):1023-1040.
4. Bairoch A, Bucher P, Hofmann K. 1996. The PROSITE database, its status in 1995. Nucleic Acids Res 24(1):189-196.
5. Bork P, Gibson TJ. 1996. Applying motif and profile searches. Methods Enzymol 266:162-184.
6. Brenner SE, Chothia C, Hubbard TJ. 1998. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 95(11):6073-6078.
7. Fischer D, Elofsson A, Rice D, Eisenberg D. 1996. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac Symp Biocomput 97:300-318.
8. Gibrat JF, Madej T, Bryant SH. 1996. Surprising similarities in structure comparison. Curr Opin Struct Biol 6(3):377-385.
9. Gribskov M, McLachlan AD, Eisenberg D. 1987. Profile analysis: Detection of distantly related proteins. Proc Natl Acad Sci USA 84(13):4355-4358.
10. Group GC. 1991. Program manual for the GCG package, version 7. (April 1991, 575 Science Drive, Madison, WI 53711).
11. Henikoff S, Henikoff JG. 1994. Position-based sequence weights. J Mol Biol 243(4):574-578.
12. Holm L, Sander C. 1998. Dictionary of recurrent domains in protein structures. Proteins 33(1):88-96.
13. Kelley LA, MacCallum RM, Sternberg M, Karplus K, Fischer D, Elofsson A, Godzik A, Rychlewski L, Pawlowski K, Jones D, et al. 1999. CAFASP-1: Critical assessment of fully automated structure prediction methods. Proteins. Forthcoming.
14. Krogh A, Mian IS, Haussler D. 1994. A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res 22(22):4768-4778.
15. Murzin AG. 1999. Structure classification-based assessment of CASP3 predictions for the fold recognition targets. Proteins Suppl 3:88-103.
16. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: A structural classification of proteins database tor the investigation of sequences and structures. J Mol Biol 247(4):536-540.
17. Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48(3):443-453.
18. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5(8):1093-1108.
19. Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. 1998. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 284(4):1201-1210.
20. Park J, Teichmann SA, Hubbard T, Chothia C. 1997. Intermediate sequences increase the detection of homology between sequences. J Mol Biol 273(1): 349-354.
21. Pawlowski K, Zhang B, Rychlewski L, Godzik A. 1999. The Helicobacter pylori genome: From sequence analysis to structural and functional predictions. Proteins 36(1):20-30.
22. Pearson WR. 1998. Empirical statistical estimates for sequence similarity searches. J Mol Biol 276(1):71-84.
23. Rychlewski L, Zhang B, Godzik A. 1998. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des 3(4):229-238.
24. Rychlewski L, Zhang B, Godzik A. 1999. Functional insights from structural predictions: Analysis of the Escherichia coli genome. Protein Sci 8(3):614-624.
25. Sander C, Schneider R. 1993. The HSSP data base of protein structure-sequence alignments. Nucleic Acids Res 21(13):3105-3109.