A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling

Journal of Computer-Aided Molecular Design

Volumn 22, Issue 11, 2008, Pages 815-829

  Arun Prasad, P ^a   Gautham, N ^a  

^a UNIVERSITY OF MADRAS   (India)

Author keywords

Computational drug design; Mean field technique; MOLS sampling; Peptide docking

Indexed keywords

LIGANDS; POTENTIAL ENERGY;

COMPUTATIONAL DRUG DESIGN; CONFORMATIONAL SPACE; DRUG DESIGN; FLEXIBLE LIGANDS; MEAN FIELD TECHNIQUE; MEAN-FIELD; MOLS SAMPLING; MUTUALLY ORTHOGONAL LATIN SQUARES; PEPTIDE DOCKING; PROTEIN RECEPTORS;

PEPTIDES;

HEPTAPEPTIDE; HEXAPEPTIDE; TETRAPEPTIDE; TRIPEPTIDE DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; COMPUTER PROGRAM; MATHEMATICAL COMPUTING; METHODOLOGY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 53249111802     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-008-9216-5     Document Type: Article

References (30)

1. Taylor RD, Jewsbury PJ, Essex JW (2002) J Comput Aided Mol Des 16:151
2. Brooijmans N, Kuntz ID (2003) Annu Rev Biophys Biomol Struct 32:335
3. Koehl P, Delarue M (1994) J Mol Biol 239:249
4. Vengadesan K, Gautham N (2003) Biophys J 84:2897
5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235
6. Vengadesan K, Gautham N (2004) Biopolymers 74:476
7. Vengadesan K, Gautham N (2004) Biochem Biophys Res Commun 316:731
8. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Proteins Struct Funct Genet 47:409
9. Bursulaya BD, Totrov M, Abagyan R, Brooks CL (2003) J Comput Aided Mol Des 17:755
10. Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST (1995) Chem Biol 2:317
11. Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA (1992) J Phys Chem 96:6472
12. Wang R, Lu Y, Wang S (2003) J Med Chem 46:2287
13. Lengauer T, Rarey M (1996) Curr Opin Struct Biol 6:402
14. Hetényi C, van der Spoel D (2002) Protein Sci 11:1729
15. Poornima CS, Dean PM (1995) J Comput Aided Mol Des 9:500
16. Chung SY, Subbiah S (1996) In: Hunter L, Klein TE, Pac Symp Biocomput. World Scientific, Hawaii, USA, pp 126-141
17. McDonald IK, Thornton JM (1994) J Mol Biol 238:777
18. Knegtel RMA, Antoon J, Rullmann C, Boelens R, Kaptein R (1994) J Mol Biol 235:318
19. Hubbard SJ, Thornton JM (1993) 'NACCESS': Computer program. Department of Biochemistry and Molecular Biology, University College, London
20. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) J Comput Chem 19:1639
21. Tame JR, Dodson EJ, Murshudov G, Higgins CF, Wilkinson AJ (1995) Structure 3:1395
22. Tame JR, Murshudov G, Dodson EJ, Neil TK, Dodson GG, Higgins CF, Wilkinson AJ (1994) Science 264:1578
23. Tame JR, Sleigh SH, Wilkinson AJ, Ladbury JE (1996) Nat Struct Biol 3:998
24. Taylor RD, Jewsbury PJ, Essex JW (2002) J Comput Chem 24:1637
25. Abagyan RA, Totrov M (1997) J Mol Biol 268:678
26. Harel M, Su C-T, Frolow F, Silman I, Sussman JL (1991) Biochemistry 30:5217
27. Rosenfeld RJ, Goodsell DS, Musah RA, Morris GM, Goodin DB, Olson AJ (2003) J Comput Aided Mol Des 17:525
28. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) J Mol Biol 267:727
29. Oberlin D, Scheraga HA (1998) J Comput Chem 19:71
30. Baysal C, Atilgan AR (2001) Proteins 45:62