Evaluation of structural similarity based on reduced dimensionality representations of protein structure

Protein Engineering, Design and Selection

Volumn 17, Issue 5, 2004, Pages 425-432

  Albrecht, Birgit ^a   Grant, Guy H ^a   Richards, W Graham ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Dimensionality reduction; Molecular similarity; Protein comparison; Sammon mapping

Indexed keywords

AMINO ACID;

ARTICLE; HUMAN; HYDROPHOBICITY; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 4644334028     PISSN: 17410126     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/gzh049     Document Type: Article

References (17)

1. Allen, B.C.P., Grant, G.H. and Richards, W.G. (2001) J. Chem. Inform. Comput. Sci., 41, 330-337.
2. Bostick, D. and Vaisman, I.I. (2003) Biochem. Biophys. Res. Commun., 304, 320-325.
3. Carbo, R.,L. and, Arnau M. (1980) Int. J. Quantum Chem., 17, 1185-1189.
4. Carugo, O. and Pongor, S. (2002) J. Mol. Biol., 315, 887-898.
5. Cserzo, M., Bernassau, J. M., Simon, I., and Maigret, B. (1994) J. Mol. Biol., 243, 388-396.
6. Downs, G.M. and Willett, P. (1995) In Boyd, D.B. (ed.), Reviews in Computational Chemistry, Vol. 7. Wiley-VCH, New York, pp. 1-66.
7. George, D.G., Barker, W.C. and Hunt, L.T. (1990) Methods Enzymol., 183, 333-351.
8. Good, A.C. and Richards, W.G. (1993) J. Chem. Inform. Comput. Sci., 33, 112-116.
9. Hodgkin, E.E. and Richards, W.G. (1987) Quantum Biol. Symp., 14, 105-110.
10. Holm, L. and Sander, C. (1992) J. Mol. Biol., 225, 93-105.
11. Holm, L. and Sander, C. (1996) Science, 273, 595-602.
12. Kolaskar, A.S. and Kulkarnikale, U. (1992) J. Mol. Biol., 223, 1053-1061.
13. Maggiora, G.M., Rohrer, D.C. and Mestres, J. (2001) J. Mol. Graph. Model., 19, 168-178.
14. Niefind, K. and Schomburg, D. (1991) J. Mol. Biol., 219, 481-497.
15. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) Structure, 5, 1093-1108.
16. Qu, C.X., Lai, L.H., Xu, X.J. and Tang, Y.Q. (1993) J. Mol. Evol., 36, 67-78.
17. Riek, R.P., Handschumacher, M.D., Sung, S.S., Tan, M., Glynias, M.J., Schluchter, M.D., Novotny, J. and Graham, R.M. (1995) J. Theor. Biol., 172, 245-258.