Inconsistent distances in substitution matrices can be avoided by properly handling hydrophobic residues

Evolutionary Bioinformatics

Volumn 2008, Issue 4, 2008, Pages 255-261

  Baussand, J ^a   Carbone, Alessandra ^a  

^a SORBONNE UNIVERSITÉ   (France)

Author keywords

Amino acids space; Hydrophobic block; Substitution matrices; Triangle inequality

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; RESIDUE ANALYSIS; SEQUENCE ALIGNMENT;

EID: 55449113269     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article

References (19)

1. Bashford, D., Chothia, C. and Lesk, A.M. 1987. Determinants of a protein fold, Unique features of the globin amino acid sequences. J. Mol. Biol., 196:199-216.
2. Baussand, J., Deremble, C. and Carbone, A. 2007. Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins. Proteins, 67:695-708.
3. Bowie, J.U., Reidhaar-Olson, J.F., Wendell, A.L. and Sauer R.T. 1990. Deciphering the message in protein sequences: tolerance to amino acids substitution. Science, 247:1306-10.
4. Callebaut, I., Renoir, J.M., Lebeau, M.C., Massol, N., Burny, A., Baulieu, E.E. and Mornon J.P. 1992. An immunophilin that binds M(r) 90,000 heat shock protein: main structural features of a mammalian p.59 protein. Proc. Natl. Acad. Sci. U.S.A., 89:6270-74.
5. Dayhoff, M.O., Schwartz, R.M. and Orcutt B.C. 1978. A model of evolutionary change in proteins, matrices for detecting distant relationships. Atlas of protein sequence and structure, National biomedical research foundation Washington DC, 5:345-58.
6. Doolittle R.F. 1981. Similar amino acid sequences: chance or common ancestry? Science, 214:149-59.
7. Friedberg, I. and Margalit H. 2001. Persistently conserved position in structurally similar sequence dissimilar proteins: roles in preserving protein fold and function. Prot. Sci., 11:350-60.
8. Gaboriaud, C., Bissery, V., Benchetrit, T. and Mornon J.P. 1987. Hydrophobic cluster analysis; an efficient new way to compare and analyse amino acid sequences. Febs. Letters, 224:149-55.
9. Henikoff, S. and Henikoff J.G. 1992. Amino acids substitution matrices from protein blocks. Proc. Natl. Acad. Sci., 89:10915-19.
10. Kinjo, A.R. and Nishikawa K. 2004. Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of mode of sequence conservation in proteins. Bioinformatics, 20:2504-08.
11. Krissinel E. 2007. On the relationship between sequence and structure similarities in proteomics. Bioinformatics, 23:717-23.
12. Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell T.L. 1992. Environnement-specific amino acids substitution tables: tertiary templates and prediction of protein folds. Prot. Sci., 1:216-26.
13. Pokarowski, P., Kloczkozski, A., Nowakowski, S., Pokarowska, M., Jernigan R.L. and Kolinski A. 2007. Ideal amino acid exchange forms for approximating substitution matrices. Proteins, 69:379-93.
14. Prlic, A., Domingues, F.S. and Prlic M.J. 2000. Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng., 13:545-50.
15. Rost B. 1999. Twilight zone of protein sequence alignments. Protein Eng., 12:85-94.
16. Stojmirovic, A. and Pestov V. 2007. Indexing schemes for similarity search in dataset of short protein fragment. Information System, 32:1145-65.
17. Vogt, G., Etzold, T., Argos P. 1995. An assessment of amino acid exchange matrices in aligning protein sequences : the twilight zone revisited. J. Mol. Biol., 249:816-31.
18. Xu, W. and Miranker D.P. 2004. A metric model of amino acid substitution Bioinformatics, 20:1214-21.
19. Xu, W. and Miranker D.P. 2004. Erratum : A metric model of amino acid substitution. Bioinformatics, 20:3716.