REFERENCES

DOCK Program References

Oshiro, C.M. and I.D. Kuntz, "Flexible ligand docking using a genetic algorithm" J. Comput-Aided Mol. Design 9, 113-130 (1995) [Full paper available]

Meng, E.C., Kuntz, I.D., Abraham, D.J., and Kellogg, G.E., "Evaluating docked complexes with the HINT exponential function and empirical atom hyrophobicities", J. Comput-Aided Mol. Design 8, 299-306 (1994)

Meng, E.C., Gschwend, D.A., Blaney, J.M., and I.D. Kuntz, "Orientational sampling and rigid-body minimization in molecular docking", Proteins: Structure, Function, and Genetics 17, 266-278 (1993)

Shoichet, B.K. and I.D. Kuntz, "Matching chemistry and shape in molecular docking", Protein Engineering 6, 223-232 (1993)

Meng, E.C., Shoichet, B.K., and I.D. Kuntz, "Automated docking with grid-based energy evaluation", J. Comp. Chem 13, 505-524 (1992)

Shoichet, B.K., Bodian, D.L, and I.D. Kuntz, "Molecular docking using shape descriptors", J. Comp. Chem. 13, 380-397 (1992)

Shoichet, B.K., and I.D. Kuntz, "Protein Docking and Complementarity ", J. Mol. Biol. 221,327-346 (1991)

DesJarlais, R.L., R.P. Sheridan, Seibel, G.L. Dixon, S., Kuntz, I.D., and Venkataraghavan, R., "Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure", J. Med. Chem. 31, 722-729 (1988)

Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and T.E. Ferrin, "A geometric approach to macromolecule-ligand interactions", J. Mol. Biol. 161, 269-288 (1982)

Chapman, B.S. and Kuntz, I.D., "Modeled structure of the 75-kDa neurotrophin receptor", Protein Science 4, 1696-1707 (1995).

Grootenhuis, P.D.J., Roe, D.C., Kollman, P.A., and Kuntz, I.D., "Finding potential DNA-binding compounds by using molecular shape", J. Comput-Aided Molec. Des. 8, 731-750 (1994)

Yamamoto, Y., Ishihara, Y., and Kuntz, I.D., "Docking analysis of a series of benzylamino acetylcholinesterase inhibitors with a phthalimide, benzoyl, or indanone moiety", J. Med. Chem. 37, 3141-3153 (1994)

Ring, C.S. Sun, E., McKerrow, J.H., Lee, G.K., Rosenthal, P.J., Kuntz, I.D., and Cohen, F.E., "Structure-based inhibitor design by using protein models for the development of antiparasitic agents", PNAS 90, 3583-3587 (1993)

Shoichet, B.K., Stroud, R.M., Santi, D.V., Kuntz,I.D., and Perry, K.M. "Structure-based discovery of inhibitors of thymidylate synthase ", Science 259, 1445-1450 (1993)

Rutenber, E., Fauman, E.B., Keenan, R.J., Fong, S., Furth, P.S., Demontellano, P.R.O., Meng, E., Kuntz, I.D., Decamp, D.L., Salto, R., Rose, J.R., Craik, C.S. and Stroud, R.M., "Structure of a non-peptide inhibitor complexed with HIV-1 Protease - developing a cycle of structure-based drug design", J. Biol. Chem. 268, 15343-15346 (1993)

Bodian, D.L., Yamasaki, R.B., Buswell, R.L., Stearns, J.F., White, J.M., and Kuntz, I.D., "Inhibition of the fusion-inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones", Biochemistry 32, 2967-78 (1993)

DesJarlais, R.L., Seibel, G.L., Kuntz, I.D., Furth, P.S., Alvarez, J.C., Ortiz de Montellano, P.R., DeCamp, D.L., Babe, L.M. and Craik, C.S. "Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease", PNAS 87, 6644-6648 (1990)

Gschwend, D.A., Good, A.C. and Kuntz, I.D., "Molecular Docking Towards Drug Discovery", J. Mol. Recognition in press (1996)

Kuntz, ID., Meng, EC, and B.K. Shoichet, "Structure-Based Strategies For Drug Design and Discovery", Acc. Chem. Res. 27, 117-123 (1994)

Kuntz, I.D., "Structure-based strategies for drug design and discovery", Science 257, 1078-1082 (1992)

BUILDER References

Lewis, R.A., Roe, D.C., Huang, C., Ferrin, T.E., Langridge, R., and I.D. Kuntz, "Automated site-directed drug design using molecular lattices", J. Mol. Graph. 10, 66-78 (1992)

Email comments and/or questions to Malin Young.