Genome analysis: Assigning protein coding regions to three-dimensional structures

Protein Science

Volumn 8, Issue 4, 1999, Pages 771-777

  Salamov, Asaf A ^a   Suwa, Makiko ^a   Orengo, Christine A ^b   Swindells, Mark B ^a,c  

^a Helix Research Institute   (Japan)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c Inpharmatica Ltd   (United Kingdom)

Author keywords

CATH; Genome analysis; Sequence search; Structure analysis

Indexed keywords

GENE PRODUCT;

AMINO ACID SEQUENCE; ARTICLE; GENOME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 0032942295     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.4.771     Document Type: Article

References (27)

1. Altschul SF, Gish W. 1996. Local alignment statistics. Methods Enzymol 266:460-480.
2. Altschul SF Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
3. 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 25:3389-3402.
4. Anneraeu J-P, Wulbrand U, Vankeerberghen A, Cuppens H, Bontems F, Tümmler B, Cassiman J-J, Stoven V. 1997. A novel model for the first nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator. FEBS Lett 407:303-308.
5. Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS. 1995. Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci USA 92:8259-8263.
6. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer based archival file for macromolecular structures. J Mol Biol 122:535-542.
7. Bowie JU, Lüthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three dimensional structure. Science 253:164-169.
8. Brenner SE, Chothia C, Hubbard TJE. 1998. Assessing sequence comparison methods with reliable structurally-identified distant evolutionary relationships. Proc Natl Acad Sci USA 95:6073-6078.
9. Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C. 1995. Challenging times for bioinformatics. Nature 376:647-648.
10. Fischer D, Eisenberg D. 1997. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 94:11929-11934.
11. Frishman D, Mewes H-W. 1997. PEDANTIC genome analysis. Trends Genet 13:415-416.
12. Gribskov M. 1992. Translational initiation factors IF-1 and eIL-α share an RNA binding motif with prokaryotic ribosomal protein S1 and polynucleotide phosphorylase. Gene 119:107-111.
13. Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919.
14. Hoedemaeker FJ, Davidson AR, Rose DR. 1998. A model for the nucleotide binding domains of ABC transporters based on the large domain of aspartate aminotransferase. Proteins 50:275-286.
15. Hyde SC, Emsley P, Hartshorn MJ, Mimmack MM, Gileadi U, Pearce SR, Gallagher MP, Gil, DR, Hubbard RE, Higgins CF. 1990. Structural model of ATP binding proteins associated with cystic fibrosis, multi-drug resistance and bacterial transport. Nature 346:366-368.
16. Jones DT, Taylor WR, Thornton JM. 1992. A new approach to fold recognition. Nature 355:86-89.
17. Jones DT, Taylor WR, Thornton JM. 1994. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33:3038-3049.
18. Jones S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM. 1998. Domain assignment for protein structures using a consensus approach: Characterization and analysis. Protein Sci 7:233-242.
19. Karlin S, Altschul SF. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 87:2264-2268.
20. Koonin E, Tatsuov RL. 1994. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. J Mol Biol 244:125-132.
21. Martin ACR, Orengo CA, Hutchinson EG, Jones S, Taroni C, Thornton JM. 1998. Protein folds and functions. Structure 6:875-884.
22. Mimura CS, Holbrook SR, Ames GF-L. 1991. Structural model of the nucleotide binding conserved component of periplasmic permeases. Proc Natl Acad Sci USA 88:84-88.
23. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5:1093-1108.
24. Park J, Teichmann SA, Hubbard T, Chothia C. 1997. Intermediate sequences increase the detection of homology between sequences. J Mol Biol 273:349-354.
25. Pearson WR, Lipman DJ. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448.
26. Rychlewski L, Zhang B, Godzik B. 1998. Fold and function predictions for Mycoplasma genitalium proteins. Folding Design 3:229-238.
27. Wooton JC. 1994. Non-globular domains in protein sequences: Automated segmentation using complexity measures. Comput Chem 18:269-285.