Multiple sequence threading: An analysis of alignment quality and stability

Journal of Molecular Biology

Volumn 269, Issue 5, 1997, Pages 902-943

  Taylor, William R ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

Alignment; Protein; Sequence; Structure; Threading

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; GENETIC PROCEDURES; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

EID: 0031588007     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1008     Document Type: Article

References (43)

1. Aszódi A., Taylor W. R. Secondary structure formation in model polypeptide chains. Protein Eng. 7:1994;633-644.
2. Aszódi A., Gradwell M. J., Taylor W. R. Global fold determination from a small number of distance restraints. J. Mol. Biol. 251:1995;308-326.
3. Bowie J. U., Clarke N. D., Pabo C. O., Sauer R. T. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Protein: Struct. Funct. Genet. 7:1990;257-264.
4. Bryant S. H. Evaluation of threading specificity and accuracy. Proteins: Struct. Funct. Genet. 26:1996;172-185.
5. 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.
6. Crawford I. P., Niermann T., Kirschner K. Prediction of secondary structure by evolutionary comparison: application to the α-subunit of tryptophan synthase. Proteins: Struct. Funct. Genet. 1:1987;118-129.
7. Dayhoff M. O., Schwartz R. M., Orcutt B. C. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure. 1978;Nat. Biomed. Res. Foundation, Washington DC.
8. Friedrichs M. S., Goldstein R. A., Wolynes P. G. Generalised protein tertiary structure recognition using associative memory Hamiltonians. J. Mol. Biol. 222:1991;1013-1034.
9. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120:1978;97-120.
10. Grandori R., Carey J. Six new candidate members of the α/β twisted, open-sheet family detected by sequence similarity to flavodoxin. Protein Sci. 3:1994;2185-2193.
11. Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
12. Jones D. T., Miller R. T., Thornton J. M. Successful protein fold recognitionby optimal sequence threading validated by rigorous blind testing. Proteins: Struct. Funct. Genet. 23:1995;387-397.
13. Lemer C. M.-R., Rooman M. J., Wodak S. J. Protein structure prediction by threading methods: evaluation of current techniques. Proteins: Struct. Funct. Genet. 23:1995;337-355.
14. Levine J. M., Pascarella S., Argos P., Garnier J. Quantification of secondary structure prediction improvement using multiple alignments. Protein Eng. 6:1993;849-854.
15. Lüthy R., Mclachlan A. D., Eisenberg D. Secondary structure-based profiles - use of structure-conserving scoring tables in searching protein-sequence databases for structural similarities. Proteins: Struct. Funct. Genet. 10:1991;229-239.
16. Madej T., Gibrat J.-F., Bryant S. H. Threading a database of protein cores. Proteins: Struct. Funct. Genet. 23:1995;356-369.
17. McClure M. A., Vasi T. K., Fitch W. M. Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol. 11:1994;571-592.
18. Murzin A. G., Brenner S. E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Mol. Biol. 247:1995;536-540.
19. Niermann T., Kirschner K. Improving the prediction of secondary structure of 'YIM-barrel' enzymes. Protein Eng. 4:1990;137-147.
20. Nishikawa K., Matsuo Y. Development for pseudoenergy potentials for assessing protein 3D-1D compatability and detecting weak homologies. Protein Eng. 6:1993;811-820.
21. Nishikawa K., Ooi T. Radial locations of amino-acid residues in a globular protein: correlation with sequence. J. Biochem. 100:1986;1043-1047.
22. Orengo C. A., Taylor W. R. A rapid method for protein structure alignment. J. Theoret. Biol. 147:1990;517-551.
23. Orengo C. A., Brown N. P., Taylor W. R. Fast protein structure comparison for databank searching. Proteins: Struct. Funct. Genet. 14:1992;139-167.
24. Pastore A., Lesk A. M. Comparison of the structures of globins and phycocyanins - evidence for evolutionary relationship. Proteins: Struct. Funct. Genet. 8:1990;133-155.
25. Rippmann F., Taylor W. R. Visualization of structural similarity in proteins. J. Mol. Graphics. 9:1991;3-16.
26. Rost B. TOPITS: Threading one-dimensional predictions into three-dimensional structures. Rawlings C., Clark D., Altman R., Hunter L., Lengauer T., Wodak S. The Third International Conference on Intelligent Systems for Molecular Biology (ISMB). 1995;AAAI Press, Menlo Park.
27. Rost B., Sander C. Progress of 1D protein structure prediction at last. Proteins: Struct. Funct. Genet. 23:1995;295-300.
28. Russell R. B., Copley R. R., Barton G. J. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259:1996;349-365.
29. Schulz G. E., Schirmer R. H. Principles of Protein Structure, 1979;Springer-Verlag.
30. Sippl M. J. Calculation of conformational ensembles from potentials of mean force an approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213:1990;859-883.
31. Taylor W. R. Identification of protein sequence homology by consensus template alignment. J. Mol. Biol. 188:1986;233-258.
32. Taylor W. R. A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28:1988;161-169.
33. Taylor W. R. Towards protein tertiary fold prediction using distance and motif constraints. Protein Eng. 4:1991;853-870.
34. Taylor W. R. Protein fold refinement: building models from idealised folds using motif constraints and multiple sequence data. Protein Eng. 6:1993;593-604.
35. Taylor W. R. Motif-biased protein sequence alignment. J. Comp. Biol. 1:1994;297-311.
36. Taylor W. R. An investigation of conservation-biased gap-penalties for multiple protein sequence alignment. Gene. 165:1995a;GC27-35. Internet journal Gene Combis: http://www.elsevier.nl/locate/genecombis.
37. Taylor W. R. Sequence alignment of proteins and nucleic acids. Meyers R. A. Encyclopedia of Molecular Biology and Biotechnology. 1995b;VCH, New York.
38. Taylor W. R. Random models for double dynamic score normalisation. J. Mol. Evol. 44:1997;S174-S180.
39. Taylor W. R., Orengo C. A. A holistic approach to protein structure comparison. Protein Eng. 2:1989a;505-519.
40. Taylor W. R., Orengo C. A. Protein structure alignment. J. Mol. Biol. 208:1989b;1-22.
41. Taylor W. R., Flores T. P., Orengo C. A. Multiple protein structure alignment. Protein Sci. 3:1994;1858-1870.
42. Thornton J. M., Taylor W. R. Protein structure prediction. Findlay J. B. C., Geisow M. J. Protein Sequencing: A Practical Approach. 1989;IRL Press, Oxford.
43. Zvelebil M. J., Barton G. J., Taylor W. R., Sternberg M. J. E. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol. 195:1987;957-961.