ALIGN_MTX-An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment

Computational Biology and Chemistry

Volumn 33, Issue 3, 2009, Pages 235-238

  Vishnepolsky, Boris ^a   Pirtskhalava, Malak ^a  

^a Institute of Molecular Biology and Biological Physics   (Georgia)

Author keywords

Sequence alignment; Substitution matrix; Text analysis; Threading

Indexed keywords

ALIGNMENT ACCURACY; AMINO ACID SEQUENCE; EVOLUTIONARY CHANGES; HYDROPHOBIC CORE; MATRIX; MULTIPLE SEQUENCE ALIGNMENTS; NUCLEOTIDE SEQUENCES; SEQUENCE ALIGNMENT; SEQUENCE ALIGNMENTS; SEQUENCE SIMILARITY; SIDE-CHAIN ORIENTATION; STRUCTURE ALIGNMENT; SUBSTITUTION MATRIX; TEXT ANALYSIS; THREADING;

AMINATION; AMINES; AMINO ACIDS; NUCLEOTIDES; ORGANIC ACIDS;

ALIGNMENT;

PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; METHODOLOGY; SEQUENCE ALIGNMENT;

PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 67349117091     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2009.04.003     Document Type: Article

References (26)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 17 (1997) 3389-3402
2. Bowie J.U., Luethy R., and Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 (1991) 164-169
3. Bryant S.H., and Lawrence C.E. An empirical energy function for threading protein sequence through the folding motif. Proteins 16 (1993) 92-112
4. Dayhoff O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure (1978), National Biomedical Research Foundation, Washington, DC 345-352
5. Domingues F.S., Lackner P., Andreeva A., and Sippl M.J. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol. 297 (2000) 1003-1013
6. Frishman D., and Argos P. Incorporation of long-distance interactions into a secondary structure prediction algorithm. Protein Eng. 9 (1996) 133-142
7. Godzik A., Kolinski A., and Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227 (1992) 227-238
8. Gonnet G.H., Cohen M.A., and Benner S.A. Exhaustive matching of the entire protein sequence database. Science 256 (1992) 1433-1445
9. Gotoh O. An improved algorithm for matching biological sequences. J. Mol. Biol. 162 (1982) 705-708
10. Gribskov M., McLachlan A.D., and Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. U.S.A. 84 (1987) 4355-4358
11. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89 (1992) 10915-10919
12. Henikoff S., and Henikoff J.G. Amino acid substitutes matrices. Adv. Protein Chem. 54 (2000) 73-96
13. Hobohm U., and Sander C. A sequence property approach to searching protein databases. J. Mol. Biol. 251 (1995) 390-399
14. Holm L., Ouzounis C., Sander C., Tuparev G., and Vriend G. A database of protein structure families with common folding motifs. Protein Sci. 1 (1992) 1691-1698
15. Jones T.D., Taylor W.R., and Thronton J.M. A new approach to protein fold recognition. Nature 358 (1992) 86-89
16. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
17. Kocher A.J.P., Rooman M.J., and Wodak S.J. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235 (1994) 1598-1613
18. Nidelman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48 (1970) 443-453
19. Ouzounis C., Sander C., Scharf M., and Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J. Mol. Biol. 232 (1993) 805-825
20. Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structures. ISMB 3 (1995) 314-321
21. Sippl M.J., and Weitckus S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins 13 (1992) 258-271
22. Sjolander K., Karplus K., Brown M., Hughet R., Krogh A., Mian I., and Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12 (1996) 327-345
23. Skolnick J., and Kihara D. Defrosting the frozen approximation: PROSPECTOR-a new approach to threading. Proteins 42 (2001) 319-331
24. Smith T.F., and Waterman M.S. The identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
25. Tan Y.H., Huang H., and Kihara D. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins 64 (2006) 587-600
26. Vishnepolsky B., Managadze G., and Pirtskhalava M. Comparison of the efficiency of evolutionary change-based and side chain orientation-based fold recognition potentials. Proteins 71 (2008) 1863-1878