Structure-dependent sequene alignment for remotely related proteins

Bioinformatics

Volumn 18, Issue 12, 2002, Pages 1658-1665

  Yang, An Suei ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; MATHEMATICAL COMPUTING; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; EVALUATION; GENETICS; METHODOLOGY; PROTEIN CONFORMATION; QUALITY CONTROL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VALIDATION STUDY;

PROTEIN;

ALGORITHMS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 0036948143     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.12.1658     Document Type: Article

References (22)

1. Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
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. Barton,G.J. and Sternberg,M.J. (1987) Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng., 1, 89-94.
4. Brenner,S.E., Chothia,C. and Hubbard,T.J. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
5. Domingues,F.S., Lackner,P., Andreeva,A. and Sippl,M.J. (2000) Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol., 297, 1003-1013.
6. Fischel-Ghodsian,F., Mathiowitz,G. and Smith,T.F. (1990) Alignment of protein sequences using secondary structure: a modified dynamic programming method. Protein Eng., 3, 577-581.
7. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
8. Hobohm,U., Scharf,M., Schneider,R. and Sander,C. (1992) Selection of representative protein data sets. Protein Sci., 1, 409-417.
9. Jaroszewski,L., Rychlewski,L. and Godzik,A. (2000) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
10. Jones,D.T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287, 797-815.
11. Kanaoka,M., Kishimoto,F., Ueki,Y. and Umeyama,H. (1989) Alignment of protein sequences using the hydrophobic core scores. Protein Eng., 2, 347-351.
12. Lesk,A.M., Levitt,M. and Chothia,C. (1986) Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng., 1, 77-78.
13. Lindahl,E. and Elofsson,A. (2000) Identification of related proteins on family, superfamily and fold level. J. Mol. Biol., 295, 613-625.
14. Marti-Renom,M.A., Stuart,A.C., Fiser,A., Sanchez,R., Melo,F. and Sali,A. (2000) Comparative protein structure modeling of gens and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291-325.
15. Miyazawa,S. and Jernigan,R.L. (2000) Identifying sequence-structure pairs undetected by sequence alignments. Protein Eng., 13, 459-475.
16. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
17. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search forsimilarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
18. Sauder,J.M., Arthur,J.W. and Dunbrack,R.L. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6-22.
19. Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
20. Yang,A.S. and Honig,B. (2000a) An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structure alignment and quantitative measure for protein structural distance. J. Mol. Biol., 301, 665-678.
21. Yang,A.S. and Honig,B. (2000b) An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol., 301, 679-690.
22. Yang,A.S. and Honig,B. (2000c) An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol., 301, 691-712.