Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase

Journal of Computer-Aided Molecular Design

Volumn 12, Issue 4, 1998, Pages 325-333

  Bliznyuk, Andrey A ^a   Gready, Jill E ^a  

^a Biology and Environment   (Australia)

Author keywords

Dihydrofolate reductase; Molecular docking; Pterin; Solvation calculation

Indexed keywords

BINDING ENERGY; BINDING SITES; POISSON EQUATION;

ACTIVE SITE; CRYSTALS STRUCTURES; DIHYDROFOLATE REDUCTASE; DOCKING SITES; ENERGY; LIGAND BINDING; MOLECULAR DOCKING; PTERIN; RIGID GEOMETRY; SOLVATION CALCULATION;

SOLVATION;

DIHYDROFOLATE REDUCTASE; LIGAND; PTERIN DERIVATIVE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; FOURIER ANALYSIS; METABOLISM; PROTEIN CONFORMATION; THERMODYNAMICS;

BINDING SITES; COMPUTER SIMULATION; FOURIER ANALYSIS; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PTERINS; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS;

EID: 0032111506     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008039000355     Document Type: Article

References (44)

1. Kollman, P.A., Curr. Opin. Struct. Biol., 4(1994) 240.
2. Aqvist, J., Medina, C. and Samuelsson, J.-E., Protein Eng., 7 (1994) 385.
3. Aqvist, J., J. Comput. Chem. 17 (1996) 1587.
4. Carlson, H.A. and Jorgensen, W.L., J. Phys. Chem., 99 (1995) 10667.
5. Gorse, A-D. and Gready, J.E., Prot. Eng., 10 (1997) 23.
6. Sharp, K.A. and Honig, B., Ann. Rev. Biophys. Biophys. Chem., 19 (1990) 301.
7. Honig, B., Sharp, K. and Yang, A., J. Phys. Chem., 97 (1993) 1101.
8. Sharp, K., Curr. Opin. Struct. Biol., 4 (1994) 234.
9. Shen, J. and Quiocho F.A., J. Comput. Chem., 16 (1995) 445.
10. Bamborough, P. and Cohen F.E., Curr. Opin. Struct. Biol., 6 (1996) 236.
11. Lengauer, T. and Rarey, M., Curr. Opin. Struct. Biol., 6 (1996) 402.
12. Lin, S.L. and Nussinov R., J. Mol. Graph., 14 (1996) 78.
13. Fischer, D., Lin, S.L., Wolfson, H.L. and Nussinov, R., J. Mol. Biol., 248 (1995) 459.
14. Kasinos, N., Lilley, G.A., Subbarao, N. and Haneel, I., Prot. Eng., 5 (1992) 69.
15. Ruppert, J., Welch, W. and Jain, A.N., Protein Science, 6 (1997), 524.
16. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C. and Vakser, I.A., Proc. Natl. Acad. Sci. USA, 89 (1992) 2195.
17. Vakser, I.A. and Aflalo, C., Proteins, 20 (1994) 320.
18. Harrison, R.W., Kourinov, I.V. and Andrews. L.C., Prot. Eng., 7 (1994) 359.
19. Bliznyuk, A.A. and Gready, J.E., J. Phys. Chem., 99 (1995) 14506.
20. Dennis, J.E., Jr. and Schnabel, R.B., Numerical methods for unconstrained optimization and nonlinear equations, Prentice Hall Inc., New York, 1983.
21. DelPhi program, Biosym Technologies version 2.5., 1993.
22. Jorgensen, W.L. and Tirado-Rives, J., J. Am. Chem. Soc., 110 (1988) 1664.
23. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz., K.M. Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Calwell, J.W. and Kollman, P.A., J. Am. Chem. Soc., 117 (1995) 5179.
24. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.D., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
25. Davies II, J.F., Delcamp, T.J., Prendergast, N.J., Ashford, V.A., Freisheim, J.H. and Kraut, J., Biochemistry, 29 (1990) 9467.
26. Oefner, C., D'Arcy, A. and Winkler, F.K., Eur.J.Biochem., 174 (1988) 377.
27. Morgan, W.D., Birdsall, B., Polshakov, V.I., Sali, D., Kompis, I. and Feeney, J., Biochemistry 34 (1995) 11690.
28. Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. and Kraut, J., J. Biol. Chem., 257 (1982) 13650.
29. McTigue, M.A., Davies II, J.F., Kaufman, B.T., Xuong, N-H. and Kraut, J., Biochemistry, 31 (1992) 7264.
30. Reyes, V.M., Sawaya, M.R., Brown, K.A. and Kraut, J., Biochemistry, 34 (1995) 2710.
31. Bystroff, C., Oatley, S.J. and Kraut, J., Biochemistry, 29 (1990) 3263.
32. Champness, J.N., Achari, A., Ballantine, S.P., Bryant, P.K., Delves, C.D. and Stammers, D.K., Structure, 2 (1994) 915.
33. Bystroff, C. and Kraut, J., Biochemistry, 30 (1991) 2227.
34. Insight II, version 95, October 1995. San Diego: Biosym/MSI, 1995.
35. Ivery, M.T.G. and Gready, J.E., Biochemistry, 34 (1995) 3724.
36. Singh, U.C. and Kollman, P.A., J. Comput. Chem., 5 (1984) 129.
37. Besler, B.H., Merz, K.M., Jr. and Kollman, P.A., J. Comput. Chem., 11 (1990) 431.
38. Gaussian 94 (Revision C.2), Frisch, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T.A., Peterson, G.A., Montgomery, J.A., Raghavachari, K., Al-Laham, M.A., Zakrzewski, V.G., Ortiz, J.V., Foresman, J.B., Cioslowski, J., Stefanov, B.B., Nanayakkara, A., Challacombe, M., Peng, C.Y., Ayala, P.Y., Chen, W., Wong, M.W., Andres, J.L., Replogle, E.S., Gomperts, R., Martin, R.L., Fox, D.J., Binkley, J.S., Defrees, D.J., Baker, J., Stewart, J.P., Head-Gordon, M., Gonzalez, C. and Pople, J.A., Gaussian, Inc., Pittsburgh P.A., 1995.
39. Pranto, J., Wiershke, S.G. and Jorgensen, W., J. Am. Chem. Soc., 113 (1991) 2810.
40. Warshel, A. Computer modelling of chemical reactions in enzymes and solutions, John Wiley and Sons, Inc., New York, 1991.
41. Sawaya, M.R. and Kraut, J., Biochemistry, 36 (1997) 586.
42. Straatsma, T.P, Zacharias, M. and McCammon, J.A., In: van Gunsteren, W.F., Weiner, P.K. and Wilkinson, A.J. (Eds.) Computer Simulation of Biomolecular Systems, Vol. 2, ESCOM, Leiden, 1993, pp. 349-367.
43. Klein, C., Chen, P., Arevalo, J.H., Stura, E.A., Marolewski, A., Warren, M.S., Benkovic, S.J. and Wilson, I.A., J. Mol. Biol., 249 (1995) 153.
44. Narayana, N., Matthews, D.A., Howell, E.E. and Xuong, N., Nature Struct. Biol., 2 (1995) 1018.