A segment alignment approach to protein comparison

Bioinformatics

Volumn 19, Issue 6, 2003, Pages 742-749

  Ye, Yuzhen ^a   Jaroszewski, Lukasz ^a   Li, Weizhong ^a   Godzik, Adam ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIMULATION;

EID: 0037433758     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg073     Document Type: Article

References (21)

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. Bystroff,C. and Baker,D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 281, 565-577.
3. Cline,M., Hughey,R. and Karplus,K. (2002) Predicting reliable regions in protein sequence alignments. Bioinformatics, 18, 306-314.
4. Gelfand,M.S., Mironov,A.A. and Pevzner,P.A. (1996) Gene recognition via spliced sequence alignment. Proc. Natl Acad. Sci. USA, 93, 9061-9066.
5. Gusfield,D. (1999) Algorithms on strings, trees and sequences: computer science and computational biology, Second edn, CUP, New York.
6. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
7. Jaroszewski,L., Li,W. and Godzik,A. (2001) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
8. Mezei,M. (1998) Chameleon sequences in the pdb. Protein Eng., 11, 411-414.
9. 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.
10. Myers,E.W. and Miller,W. (1988) Optimal alignments in linear space. CABIOS, 4, 11-17.
11. Novichkov,P.S., Gelfand,M.S. and Mironov,A.A. (2001) Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics, 17, 1011-1018.
12. Ogata,K., Morikawa,S., Nakamura,H., Sekikawa,A., Inoue,T., Kanai,H., Sarai,A., Ishii,S. and Nishimura,Y. (1994) Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell, 79, 639-648.
13. Rost,B. (1997) Protein structures sustain evolutionary drift. Fold Des., 2, S19-24.
14. Rychlewski,L. and Godzik,A. (1997) Secondary structure prediction using segment similarity. Protein Eng., 10, 1143-1153.
15. Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
16. Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257.
17. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
18. Simons,K.T., Bonneau,R., Ruczinski,I.I. and Baker,D. (1999) Ab initio protein structure prediction of CASP III targets using rosetta. Proteins, 37, 171-176.
19. Sternberg,M.J., Bates,P.A., Kelley,L.A. and MacCallum,R.M. (1999) Progress in protein structure prediction: assessment of CASP3. Curr Opin. Struct. Biol., 9, 368-373.
20. Waterman,M.S. (1995) Introduction to Computational Biology, First edn, Chapman and Hall, London, pp. 183-228.
21. Yi,T.M. and Lander,E.S. (1993) Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol., 232, 1117-1129.