Identification of the bioactive conformation for mucin epitope peptides

Journal of Molecular Structure: THEOCHEM

Volumn 823, Issue 1-3, 2007, Pages 16-27

  Kalaszi, Adrian ^a   Imre, Gabor ^a   Jakli, Imre ^a   Farkas, Odon ^a  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Binding free energy; Bioactive structures; Conformational flexibility; Conformational search; Drug design; Molecular dynamics; Rational library design

Indexed keywords

EID: 35348918437     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.theochem.2007.08.016     Document Type: Article

References (34)

1. Kim Y.S., Gum J.R., Byrd J.C., and Toribara N.W. Am. Rev. Respir. Dis. 144 (1991) S10-S14
2. Uray K., Price M.R., Majer Z., Vass E., Hollosi M., and Hudecz F. Arch. Biochem. Biophys. 410 (2003) 254
3. Windberg E., Uray K., Illyes E., Skribanek Z., Price M.R., Sebestyen F., and Hudecz F. J. Pept. Sci. 10 (2004) 56
4. Hopfinger A.J., Wang S., Tokarski J.S., Jin B.Q., Albuquerque M., Madhav P.J., and Duraiswami C. J. Am. Chem. Soc. 119 (1997) 10509
5. Streich D., Neuburger-Zehnder M., and Vedani A. Quant. Struct-Act. Rel. 19 (2001) 565
6. Vedani A., Dobler M., and Zbinden P. J. Am. Chem. Soc. 120 (1998) 4471
7. Vedani A., Briem K., Dobler M., Dollinger H., and McMasters D.R. J. Med. Chem. 43 (2000) 4416
8. Vedani A., McMasters D.R., and Dobler M. Quant. Struct.-Act. Rel. 19 (2000) 149
9. Vedani A., and Dobler M. J. Med. Chem. 45 (2002) 2139
10. Martinek T.A., Otvos F., Dervarics M., Toth G., and Fulop F. J. Med. Chem. 48 (2005) 3239
11. Dervarics M., Otvos F., and Martinek T.A. J. Chem. Inf. Model. 46 (2006) 1431
12. Bernard D., Coop A., and Mackerell A.D. J. Med. Chem. 48 (2005) 7773
13. Bernard D., Coop A., and Mackerell A.D. J. Am. Chem. Soc. 125 (2003) 3101
14. Martinek T.A., Otvos F., Dervarics M., Toth G., and Fulop F. J. Med. Chem. 48 (2005) 3239
15. Dervarics M., Otvos F., and Martinek T.A. J. Chem. Inf. Model. 46 (2006) 1431
16. Janssen L.H.M. Bioorg. Med. Chem. 6 (1998) 785
17. Searle M.S., and Williams D.H. J. Am. Chem. Soc. 114 (1992) 10690
18. Vedani A., and Dobler M. Quant. Struct.-Act. Rel. 21 (2002) 382
19. M. Manea, A. Kalaszi, G. Mezo, K. Horvati, A. Horvath, O. Farkas, M. Przybylski, F. Hudecz, J. Med. Chem., submitted for publication.
20. Cheng Y.C., and Prusoff W.H. Biochem. Pharmacol. 22 (1973) 3099
21. Hawkins D.M. J. Chem. Inf. Comput. Sci. 44 (2004) 1
22. D.J. Heisterberg, http://www.ccl.net/cca/software/SOURCES/C/quaternion-mol-fit/quatfit.c (1990).
23. Kalászi A., and Farkas O. J. Mol. Struct.-Theochem 666 (2003) 645
24. Barnard J.M., and Downs G.M. J. Chem. Inf. Comput. Sci. 37 (1997) 141
25. Brown R.D., and Martin Y.C. J. Chem. Inf. Comput. Sci. 36 (1996) 572
26. ChemAxon, MarvinBeans, http://www/chemaxon.com (2007).
27. Windberg E., Uray K., Illyes E., Skribanek Z., Price M.R., Sebestyen F., and Hudecz F. J. Pept. Sci. 10 (2004) 56
28. Berendsen H.J.C., Vanderspoel D., and Vandrunen R. Comput. Phys. Commun. 91 (1995) 43
29. Lindahl E., Hess B., and van der Spoel D. J. Mol. Model. 7 (2001) 306
30. van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J.C. J. Comput. Chem. 26 (2005) 1701
31. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. J. Comput. Chem. 18 (1997) 1463
32. Perola E., and Charifson P.S. J. Med. Chem. 47 (2004) 2499
33. Singh N., Cheve G., Ferguson D.M., and McCurdy C.R. J. Comput. Aided. Mol. Des. 20 (2006) 471
34. Golbraikh A., and Tropsha A. J. Mol. Graph. Model. 20 (2002) 269