WebProAnalyst: An interactive tool for analysis of quantitative structure-activity relationships in protein families

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Ivanisenko, Vladimir A ^a,b   Eroshkin, Alexey M ^c   Kolchanov, Nickolay A ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^c STATE RESEARCH CENTER OF VIROLOGY AND BIOTECHNOLOGY VECTOR   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

HISTATIN; POLYPEPTIDE ANTIBIOTIC AGENT; ANTIMICROBIAL CATIONIC PEPTIDE; M2 PROTEIN, INFLUENZA A VIRUS; MATRIX PROTEIN; PROTEIN;

ACCESS TO INFORMATION; ALPHA HELIX; AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; CANDIDA ALBICANS; COMPUTER PROGRAM; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; EXPERIMENTATION; FUNGICIDAL ACTIVITY; HYDROPHOBICITY; INTERNET; MULTIPLE LINEAR REGRESSION ANALYSIS; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; REGRESSION ANALYSIS; STRUCTURE ACTIVITY RELATION; CHEMISTRY; CLASSIFICATION; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION; DATA ANALYSIS SOFTWARE; EXPERIMENTAL DESIGN; KINETICS; PROCESS DESIGN; SEARCH ENGINE;

CANDIDA ALBICANS;

ANTIMICROBIAL CATIONIC PEPTIDES; INTERNET; PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE; VIRAL MATRIX PROTEINS;

EID: 23144436395     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki421     Document Type: Article

References (23)

1. Hughes,T.R., Robinson,M.D., Mitsakakis,N. and Johnston,M. (2004) The promise of functional genomics: Completing the encyclopedia of a cell. Curr. Opin. Microbiol., 7, 546-554.
2. Mihalek,I., Res,I. and Lichtarge,O. (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J. Mol. Biol., 336, 1265-1282.
3. Livingstone,C.D. and Barton,G.J. (1993) Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745-756.
4. Kalinina,O.V., Novichkov,P.S., Mironov,A.A., Gelfand,M.S. and Rakhmaninova,A.B. (2004) SDPpred: A tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res., 32, W424-W428.
5. Lejon,T., Strom,M.B. and Svendsen,J.S. (2001) Antibiotic activity of pentadecapeptides modelled from amino acid descriptors. J. Pept. Sci., 7, 74-81.
6. Sandberg,M., Eriksson,L., Jonsson,J., Sjostrom,M. and Wold,S. (1998) New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J. Med. Chem., 41, 2481-2491.
7. Norinder,U., Rivera,C. and Unden,A. (1997) A quantitative structure-activity relationship study of some substance P-related peptides. A multivariate approach using PLS and variable selection. J. Pept. Res., 49, 155-162.
8. Ivanisenko,V.A. and Eroshkin,A.M. (1997) Search for sites with functionally important substitutions in sets of related or mutant protein. Mol. Biol. (Moskow), 31, 749-755.
9. Eroshkin,A.M., Fomin,V.I., Zhilkin,P.A., Ivanisenko,V.A. and Kondrakhin,Y.V. (1995) PROANAL version 2: Multifunctional program for analysis of multiple protein sequence alignments and studying structure-activity relationships in protein families. Comput. Appl. Biosci., 11, 39-44.
10. Eroshkin,A.M., Zhilkin,P.A. and Fomin,V.I. (1993) Algorithm and computer program Pro_Anal for analysis of relationship between structure and activity in a family of proteins or peptides. Comput. Appl. Biosci., 9, 491-497.
11. Draper,N.R. and Smith,H. (1998) Applied Regression Analysis, 3rd edn. John Wiley and Sons, NY.
12. Rumelhart,D.E., Hinton,G.E. and Williams,R.J. (1986) Learning internal representations by error propagation. In Rumelhart,D.E. and McClelland,J.L. (eds), Parallel Distributed Processing. MIT Press, Cambridge Vol. 1, pp. 318-362.
13. Hay,A.J. (1992) The action of adamantanamines against influenza A viruses: Inhibition of the M2 ion channel protein. Semin. Virol., 3, 21-30.
14. Chizhmakov,I.V., Geraghty,F.M., Ogden,D.C., Hayhurst,A., Antoniou,M. and Hay,A.J. (1996) Selective proton permeability and pH regulation of the influenza virus M2 channel expressed in mouse erythroleukaemia cells. J. Physiol., 494, 329-336.
15. Kiselev,O.I., Mishin,V.P., Eroshkin,V.I., Kozeletskaia,K.N., Usova,E.V., Rudenko,V.I. and Chupakhin,O.N. (1994) Secondary structure of the M2 protein of influenza type A virus and its role in forming resistance to rimantadine and deitiforin. Mol. Biol. (Moskow), 28, 1009-1013.
16. Duff,K.C., Gilchrist,P.J., Saxena,A.M. and Bradshaw,J.P. (1994) Neutron-diffraction reveals the site of amantadine blockade in the influenza-A M2 ion-channel. Virology, 202, 287-293.
17. Sansom,M.S.P. and Kerr,I.D. (1993) Influenza virus M2 protein: A molecular modelling study of the ion channel. Protein Eng., 6, 65-74.
18. Tian,C., Gao,P.F., Pinto,L.H., Lamb,R.A. and Cross,T.A. (2003) Initial structural and dynamic characterization of the M2 protein transmembrane and amphipathic helices in lipid bilayers. Protein Sci., 12, 2597-2605.
19. Helmerhorst,E.J., Van't Hof,W., Veerman,E.C., Simoons-Smit,I. and Nieuw Amerongen,A.V. (1997) Synthetic histatin analogues with broad-spectrum antimicrobial activity. Biochem. J., 326, 39-45.
20. Ivanisenko,V.A., Pintus,S.S., Grigorovich,D.A. and Kolchanov,NA. (2005) PDBSite: A database of the 3D structure of protein functional sites. Nucleic Acids Res., 33, D183-D187.
21. Ivanisenko,V.A., Pintus,S.S., Grigorovich,D.A. and Kolchanov,N.A. (2004) PDBSiteScan: A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res., 32, W549-W554.
22. Fliri,A.F., Loging,W.T., Thadeio,P.F. and Volkmann,R.A. (2005) Biological spectra analysis: Linking biological activity profiles to molecular structure. Proc. Natl Acad. Sci. USA, 102, 261-266.
23. Liu,Y., Patricelli,M.P. and Cravatt,B.F. (1999) Activity-based protein profiling: The serine hydrolases. Proc. Natl Acad. Sci. USA, 96, 14694-14699.