3DCoffee: Combining protein sequences and structures within multiple sequence alignments

Journal of Molecular Biology

Volumn 340, Issue 2, 2004, Pages 385-395

  O'Sullivan, Orla ^a   Suhre, Karsten ^b   Abergel, Chantal ^b   Higgins, Desmond G ^a   Notredame, Cédric ^b,c  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b CNRS Aix Marseille University   (France)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

CS, column score; DP, dynamic programming; MSA, multiple protein sequence alignment(s); multiple alignment; NW, Needlman Wunsch; S MSA, structure based MSA; sap; structural superposition; TCoffee; threading

Indexed keywords

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CORRELATION ANALYSIS; INFORMATION PROCESSING; LINEAR REGRESSION ANALYSIS; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; SEQUENCE ALIGNMENT; THEORETICAL MODEL;

EID: 2942619012     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.058     Document Type: Article

References (43)

1. Lesk A.M., Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 136:1980;225-270
2. Al-Lazikani B., Sheinerman F.B., Honig B. Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. Proc. Natl Acad. Sci. USA. 98:2001;14796-14801
3. Marchler-Bauer A., Panchenko A.R., Ariel N., Bryant S.H. Comparison of sequence and structure alignments for protein domains. Proteins: Struct. Funct. Genet. 48:2002;439-446
4. Brenner S.E. A tour of structural genomics. Nature Rev. Genet. 2:2001;801-809
5. Duret L., Abdeddaim S. Multiple alignment for structural, functional, or phylogenetic analyses of homologous sequences. Higgins D., Taylor W. Bioinformatics, Sequence, Structure and Databanks. 2000;135-147 Oxford University Press, Oxford
6. Ng P.C., Henikoff S. Accounting for human polymorphisms predicted to affect protein function. Genome Res. 12:2002;436-446
7. Wang L., Jiang T. On the complexity of multiple sequence alignment. J. Comput. Biol. 1:1994;337-348
8. Thompson J.D., Plewniak F., Ripp R., Thierry J.C., Poch O. Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol. 314:2001;937-951
9. Lipman D.J., Altschul S.F., Kececioglu J.D. A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA. 86:1989;4412-4415
10. Hogeweg P., Hesper B. The alignment of sets of sequences and the construction of phylogenetic trees. An integrated method. J. Mol. Evol. 20:1984;175-186
11. Mizuguchi K., Deane C.M., Blundell T.L., Overington J.P. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7:1998;2469-2471
12. Raghava G.P., Searle S.M., Audley P.C., Barber J.D., Barton G.J. OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics. 4:2003;47
13. Thompson J.D., Plewniak F., Poch O. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics. 15:1999;87-88
14. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl. Acids Res. 30:2002;3059-3066
15. Lassmann T., Sonnhammer E.L. Quality assessment of multiple alignment programs. FEBS Letters. 529:2002;126-130
16. Lee C., Grasso C., Sharlow M.F. Multiple sequence alignment using partial order graphs. Bioinformatics. 18:2002;452-464
17. Thompson J.D., Plewniak F., Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucl. Acids Res. 27:1999;2682-2690
18. Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:1970;443-453
19. Pearson W.R., Miller W. Dynamic programming algorithms for biological sequence comparison. Methods Enzymol. 210:1992;575-601
20. Huang X., Hardison R.C., Miller W. A space-efficient algorithm for local similarities. Comput. Appl. Biosci. 6:1990;373-381
21. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197
22. Brenner S.E., Chothia C., Hubbard T.J. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA. 95:1998;6073-6078
23. Eidhammer I., Jonassen I., Taylor W.R. Structure comparison and structure patterns. J. Comput. Biol. 7:2000;685-716
24. Sillitoe I., Orengo C. Protein structure comparison. Orengo C., Jones D., Thornton J. Bioinformatics: genes, proteins and computers. 2002;250-265 BIOS Scientific Publisher, Oxford
25. Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A. 34:1978;827-828
26. Russell R.B., Barton G.J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins: Struct. Funct. Genet. 14:1992;309-323
27. Taylor W.R., Orengo C.A. Protein structure alignment. J. Mol. Biol. 208:1989;1-22
28. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138
29. Jones D.T., Orengo C.A., Thornton J.M. Sternberg M.J.E. Protein Folds and their Recognition From Sequence. 1st edit. Protein Structure Prediction. vol. 170:1996;173-206 Oxford University Press, Oxford
30. Cristobal S., Zemla A., Fischer D., Rychlewski L., Elofsson A. A study of quality measures for protein threading models. BMC Bioinform. 2:2001;5
31. Bryant S.H., Lawrence C.E. An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16:1993;92-112
32. Shi J., Blundell T.L., Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310:2001;243-257
33. Taylor W.R., Flores T.P., Orengo C.A. Multiple protein structure alignment. Protein Sci. 3:1994;1858-1870
34. Sali A., Blundell T.L. Definition of general topological equivalence in protein structures. J. Mol. Biol. 212:1990;403-428
35. Sutcliffe M.J., Haneef I., Carney D., Blundell T.L. Knowledge based modelling of homologous proteins. Part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1:1987;377-384
36. Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:2000;205-217
37. Huang X., Miller W. A time-efficient, linear-space local similarity algorithm. Advan. Appl. Math. 12:1991;337-357
38. Thompson J., Higgins D., Gibson T. CLUSTAL W.: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4690
39. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425
40. Jones T.A., Kleywegt G.J. CASP3 comparative modeling evaluation. Proteins: Struct. Funct. Genet. Suppl. 3:1999;30-46
41. Karplus K., Hu B. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics. 17:2001;713-720
42. Bourne P.E. CASP and CAFASP experiments and their findings. Methods Biochem. Anal. 44:2003;501-507
43. Vitkup D., Melamud E., Moult J., Sander C. Completeness in structural genomics. Nature Struct. Biol. 8:2001;559-566