Factor analysis scales of generalized amino acid information as applied in predicting interactions between the human amphiphysin-1 SH3 domains and their peptide ligands

Chemical Biology and Drug Design

Volumn 71, Issue 4, 2008, Pages 345-351

  Liang, Guizhao ^a   Chen, Guohua ^a   Niu, Weihuan ^a   Li, Zhiliang ^a  

^a CHONGQING UNIVERSITY   (China)

Author keywords

Amphiphysin 1; Factor analysis scale of generalized amino acid information; Genetic algorithm; Partial least square; Quantitative structure affinity relationship; SH3 domain

Indexed keywords

AMPHIPHYSIN; AMPHIPHYSIN 1 SH3; PEPTIDE; PROTEIN SH3; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BINDING AFFINITY; CORRELATION ANALYSIS; ELECTRONICS; FACTOR ANALYSIS SCALES OF GENERALIZED AMINO ACID INFORMATION; FACTORIAL ANALYSIS; GENETIC ALGORITHM; HYDROPHOBICITY; MATHEMATICAL COMPUTING; PARTIAL LEAST SQUARES REGRESSION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

EID: 40449106762     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2008.00641.x     Document Type: Article

References (19)

1. 1 Dalgarno D.C., Botfield M.C., Rickles R.J. (1997) SH3 domains and drug design: ligands, structure, and biological function. Biopolymers ; 43: 383–400.
2. 2 Ren R., Mayer B.J., Cicchetti P., Baltimore D. (1993) Identification of a 10‐amino acid proline‐rich SH3 binding‐site. Science ; 259: 1157–1161.
3. 3 Slepnev V.I., Ochoa G.C., Butler M.H., Grabs D., De Camilli P. (1998) Role of phosphorylation in regulation of the assembly of endocytic coat complexes. Science ; 281: 821–824.
4. 4 Rickles R.J., Botfield M.C., Zhou X., Henry P.A., Brugge J.S. (1995) Phage display selection of ligand residues important for Src homology 3 domain binding specificity. Proc Natl Acad Sci U S A ; 92: 10909–10913.
5. 5 Wang W., Lim W.A., Jakalian A., Wang J., Wang J.M., Luo R., Bayly C.I., Kollman P.A. (2001) An analysis of the interactions between the Sem‐5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. J Am Chem Soc ; 123: 3986–3994.
6. 6 Doytchinova I.A., Flower D.R. (2001) Toward the quantitative prediction of T‐cell epitopes: CoMFA and CoMSIA studies of peptides with affinity for the class I MHC molecule HLA‐A*0201. J Med Chem ; 44: 3572–3581.
7. 7 Hou T.J., McLaughlin W., Lu B.Z., Chen K., Wang W. (2006) Prediction of binding affinities between the human amphiphysin‐1 SH3 domain and Its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res ; 5: 32–43.
8. 8 Anfinsen C.B. (1973) Principles that govern the folding of protein chains. Science ; 181: 223–230.
9. 9 Kawashima S., Kanehisa M. (2000) AAindex: amino acid index database. Nucleic Acids Res ; 28: 374.
10. 10 Tomii K., Kanehisa M. (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng ; 9: 27–36.
11. 11 Nakai K., Kidera A., Kanehisa M. (1988) Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng ; 2: 93–100.
12. 12 Johnson R.A., Wichern D.W. (2002) Applied Multivariate Statistical Analysis. Upper Saddle River: Prentice Hall.
13. 13 Landgraf C., Panni S., Montecchi‐Palazzi L., Castagnoli L., Schneider‐Mergener J., Volkmer‐Engert R., Cesareni G. (2004) Protein interaction networks by proteome peptide scanning. PLoS Biol ; 2: 94–103.
14. 14 Hasegawa K., Funatsu K. (1998) GA strategy for variable selection in QSAR studies: GAPLS and D‐optimal designs for predictive QSAR model. J Mol Struct (Theochem) ; 425: 255–262.
15. 15 Hasegawa K., Kimura T., Funatsu K. (1999) GA strategy for variable selection in QSAR studies: Enhancement of comparative molecular binding energy analysis by GA‐based PLS method. Quant Struct Activ Relat ; 18: 262–272.
16. 16 Hasegawa K., Miyashita Y., Funatsu K. (1997) GA strategy for variable selection in QSAR studies: GA based PLS analysis of calcium channel antagonists. J Chem Inf Comput Sci ; 37: 306–310.
17. 17 Golbraikh A., Tropsha A. (2002) Beware of q 2 !. J Mol Graphics Mod ; 20: 269–276.
18. 18 Wold S., Sjöström M., Eriksson L. (2001) PLS‐Regression: A basic tool of chemometrics. Chemom Intell Lab Syst ; 58: 109–130.
19. 19 Wold S., Trygg J., Berglund A., Antti H. (2001) Some recent developments in PLS modeling. Chemom Intell Lab Syst ; 58: 131–150.