AAindex: Amino acid index database, progress report 2008

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Kawashima, Shuichi ^a   Pokarowski, Piotr ^b   Pokarowska, Maria ^c   Kolinski, Andrzej ^d   Katayama, Toshiaki ^a   Kanehisa, Minoru ^a,e  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF WARSAW   (Poland)

^c WARSAW UNIVERSITY OF TECHNOLOGY   (Poland)

^d UNIVERSITY OF WARSAW   (Poland)

^e KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AAINDEX; AMINO ACID INDEX DATABASE; AMINO ACID SUBSTITUTION; ARTICLE; BIOCHEMISTRY; BIOINFORMATICS; HYDROPHOBICITY; INFORMATION; INTERNET; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN DATABASE;

AMINO ACIDS; DATABASES, PROTEIN; INTERNET; PROTEINS;

EID: 38549155006     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm998     Document Type: Article

References (16)

1. Nakai, K., Kidera, A. and Kanehisa, M. (1988) Cluster analysis of amino acid indices for prediction, of-protein structure and-function. Protein Eng., 2, 93-100.
2. Tomii, K. and Kanehisa, M. (1996) Analysis of amino, acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng., 9, 27-36.
3. Kawashima, S., Ogata, H. and Kanehisa, M. (1999) AAindex: Amino acid index database. Nucleic Acids Res., 27, 368-369.
4. Kawashima, S. and Kanehisa, M. (2000) AAIndex: Amino acid index database. Nucleic Acids Res., 28, 374.
5. Sarda, D, Chua, G.H., Li, K-B. and Krishnan, A. (2005) pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties. BMC Bioinformatics, 6, 152.
6. Tung, C.-W. and Ho, S.-Y, (2007) POPI: Predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. Bioinformatics, 23, 942-949.
7. Liu, B., Li, S, Wang, Y., c, Lu, L., Li, Y. and Cai, Y. (2007) Predicting the protein SUMO modification sites based on properties sequential forward selection (PSFS). Biochem. Biophys. Res. Comm., 358, 136-139.
8. Afonnikov, D.A. and Kolchanov, N.A. (2004) CRASP: A program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucleic Acids Res., 32, W64-W68.
9. Bulka, B., desJardins, M. and Freeland, S.J. (2006) An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices. BMC Bioinformatics, 7, 329.
10. Pokarowski, P., Kloczkowski, A., Jernigan, R.L., Kothari, N.S., Pokarowska, M. and Kolinski, A. (2005) Inferring ideal amino acid interaction forms from statistical protein contact potentials. Proteins, 59, 49-57.
11. Miyazawa, S. and Jernigan, R.J. (1999) Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins, 34, 49-68.
12. Pokarowski, P., Kloczkowski, A., Nowakowski, S., Pokarowska, M., Jernigan, R.L. and Kolinski, A. (2007) Ideal amino acid exchange forms for approximating substitution matrices. Proteins, 69, 379-393.
13. Seto, Y., Ihara, S., Kohtsuki, S, Ooi, T. and Sakakibara, S. (1988) Peptide and protein databanks in Japan. In Lesk, A.M. (ed.), Computational Molecular Biology, Oxford University Press, Oxford, pp. 27-37.
14. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y. and Kanehisa, M. (1998) DBGET/LinkDB: An integrated database retrieval system. Pacific Symp. Biocomput. 1998, 683-694.
15. Kanehisa, M. (1997) Linking databases and organisms: GenomeNet resources in japan. Trends Biochem. Sci., 22, 442-444.
16. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: The European molecular biology open software suite. Trends Genet., 16, 276-277.