Classic Dock References

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DesJarlais, R.L. and Dixon, J.S. A Shape-and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors. J. Comput-Aided Molec. Design. 8: 231-242, 1994.

Ewing, T.J.A. and Kuntz, I.D., Critical evaluation of search algorithms for automated molecular docking and database screening. J. Comput. Chem. 18: 1175-1189, 1997.

Ferro, D.R. and Hermans, J. Different best rigid-body molecular fit routine. Acta. Cryst. A. 33: 345-347,1977.

Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise Solute Descreening of Solute Charges from a Dielectric Medium. Chem. Phys. Lett. 246: 122-129, 1995

Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100: 19824-19839, 1996

Irwin, J.J. and Shoichet, B.K. ZINC - A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45: 177-182, 2005.

Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res.33: 889-897, 2000

Kuhl, F.S., Crippen, G.M., and Friesen, D.K. A Combinatorial Algorithm for Calculating Ligand Binding. J. Comput. Chem. 5:24-34, 1984.

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

Liu, H.-Y., Kuntz, I. D., and Zou, X. Pairwise GB/SA Scoring Function for Structure-based Drug Design. J. Phys. Chem. B. 108: 5453-5462, 2004.

Luty, B. A.; Wasserman P.F.; Hodge C.N.; Zacharias M.; McCammon J.A. A Molecular Mechanics / Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. 16:454-464 (1995)

Meng, E.C., Gschwend, D.A., Blaney, J.M. and Kuntz, I.D. Orientational sampling and rigid-body minimization in molecular docking. Proteins. 17(3): 266-278, 1993.

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

Miller, M.D., Kearsley, S.K., Underwood, D.J. and Sheridan, R.P. FLOG -A system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure. J. Comput. Aided Mol. Design. 8: 153-174, 1994.

Moustakas, D.T., Lang, P.T., Pegg, S., Pettersen, E.T., Kuntz, I.D., Broojimans, N., Rizzo, R.C. Development and Validation of a Modular, Extensible Docking Program: DOCK 5. submitted. 2006.

Nelder, J.A. and Mead, R., A Simplex-Method for Function Minimization. Computer Journal, 7: 308-313, 1964.

Onufriev, A., Bashford, D., and Case, D.A. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins. 55:383-394, 2004.

Pearlman, D.A., Case, D.A.,Caldwell, J.W., Ross, W.S., Cheatham, III, T.E., DeBolt, S., Ferguson, D., Seibel, G. and Kollman, P.A. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91:1-41, 1995.

Rizzo, R. C. ; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory Comput . 2: 128-139, 2006

Shoichet, B.K., Bodian, D.L. and Kuntz, I.D. Molecular docking using shape descriptors. J. Comp. Chem. 13(3): 380-397, 1992.

Shoichet, B.K. and Kuntz, I.D. Protein docking and complementarity. J. Mol. Biol. 221: 327-346, 1991.

Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A., Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 120:9401-9409, 1998.

Tsui, V. and Case,D.A. Theory and applications of the generalized solvation model in macromolecular simulations. Biopolymers. 56:275-291, 2001.

Verkhiver, G.M.; Rejto, P.A.; Bouzida, D.; Arthur, S.; Colson, A.B.; et. al. Towards Understanding the Mechanisms of Molecular Recognition by Computer Simulation of Ligand-Protein Interactions. J. Mol. Recog. 12:371-389 (1999)

Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A. and Case, D.A. Development and testing of a general Amber force field. J. Comput. Chem. 25:1157-1174, 2004.

Weiser, J., Shenkin, P.S., and Still, W.C. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J. Comput. Chem. 20:217-230, 1999.

Zou, X. Q., Sun, Y. X., and Kuntz, I. D. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model. J. Am. Chem. Soc. 121 (35): 8033-8043, 1999.