Estimation of atomic hydrophobicities using molecular dynamics simulation of peptides

Progress in Biomedical Optics and Imaging - Proceedings of SPIE

Volumn 6799, Issue , 2008, Pages

  Held, Marie ^a   Nicolau, Dan V ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

Atom level; Hydrophobicity scales; Molecular dynamics; Peptide

Indexed keywords

AMINO ACIDS; BINDING SITES; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTIONS; MOLECULAR MODELING; PROTEIN FOLDING;

ATOM LEVEL HYDROPHOBICITY; HYDROPHOBICITY SCALES;

PEPTIDES;

EID: 43049098200     PISSN: 16057422     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1117/12.759385     Document Type: Conference Paper

References (21)

1. G. Schneider and U. Fechner, "Computer-based de novo design of drug-like molecules," Nat. Rev. Drug Discov. 4(8), 649-663 (2005)
2. A. Pallandre, B. DeMeersman, F. Blondeau, B. Nysten and A. M. Jonas, "Tuning the Orientation of an Antigen by Adsorption onto Nanostriped Templates," Journal of the American Chemical Society 127(12), 4320-4325 (2005)
3. F. A. Denis, P. Hanarp, D. S. Sutherland, J. Gold, C. Mustin, P. G. Rouxhet and Y. F. Dufrene, "Protein Adsorption on Model Surfaces with Controlled Nanotopography and Chemistry," Langmuir 18(3), 819-828 (2002)
4. C. B. Anfinsen, "The formation and stabilization of protein structure," Journal of Chemical Physics 128(4), 737-749 (1972)
5. F. M. Richards, "The protein folding problem," Scientific American 264(1), 54-60 (1991)
6. J. U. Bowie, R. Luthy and D. Eisenberg, "A method to identify protein sequences that fold into a known three-dimensional structure," Science 253(164-170), (1991)
7. K. A. Dill and K. Yue, "Inverse protein folding problem: designing polymer sequences," Proc. Natl. Acad. Sci. USA 89(9), 4163-4167 (1992)
8. W. Kauzmann, "Some factors in the interpretation of protein denaturation," Advances in Protein Chemistry 14(1-60 (1959)
9. B. Lee and F. M. Richards, "The interpretation of protein structures: Estimation of static accessibility," Journal of Molecular Biology 55(3), 379-380 (1971)
10. M. L. Connolly, "Solvent-accessible surfaces of proteins and nucleic acids," Science 221(4612), 709-713 (1983)
11. D. V. Nicolau, F. Fulga and D. V. Nicolau, "A new program to compute the surface properties of biomolecules," Asia-pacific Biotech 7(3), 29-34 (2003)
12. D. V. Nicolau and D. V. Nicolau, "A database comprising biomolecular descriptors relevant to protein adsorption on microarray surfaces," Proc. SPIE 4626(109-115 (2002)
13. D. V. Nicolau and D. V. Nicolau, "Towards a Theory of Protein Adsorption: Predicting the Adsorption of Proteins on Surfaces Using a Piecewise Linear Model Validated Using the Biomolecular Adsorption Database," 2nd Asia-Pacific Bioinformatics Conference; Conferences in Research and Practice in Information Technology Vol. 29 (2004)
14. J. Kyte and R. F. Doolittle, "A simple method for displaying the hydropathic character of a protein," Journal of Molecular Biology 157(1), 105-132 (1982)
15. P. Furet, A. Sele and N. C. Cohen, "3D molecular lipophilicity potential profiles: a new tool in molecular modeling," Journal of Molecular Graphics 6(4), 182-189 (1988)
16. E. Audry, J. P. Dubost, J. C. Colleter and P. Dallet, Eur. J. Med. Chem.-Chim. Ther. 21(71-72 (1986)
17. W. C. Wimley, T. P. Creamer and S. H. White, "Solvation Energies of Amino Acid Side Chains and Backbone in a Family of Host-Guest Pentapeptides," Biochemistry 35(16), 5109-5124 (1996)
18. S. H. White and W. C. Wimley, "Hydrophobic interactions of peptides with membrane interfaces," Biochimica and Biophysica Acta 1376(339-352 (1998)
19. W. C. Wimley and S. H. White, "Experimentally determined hydrophobicity scale for proteins at membrane interfaces," Nat Struct Mol Biol 3(10), 842-848 (1996)
20. G. E. Kellogg, S. F. Semus and D. J. Abraham, "HrNT: A new method of empirical hydrophobic field calculation for CoMFA," Journal of Computer-Aided Molecular Design 5(6), 545-552 (1991)
21. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations," Journal of Computational Chemistry 4(2), 187-217(1983)