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	"High Spin Reactivity Under Ambient Conditions: An Ultrafast UV-Pump IR-Probe Study" Snee, P. T.; Payne, C. K.; Kotz, K. T.; Yang, H.; Harris, C. B., J. Am. Chem. Soc., 2001, 123, 2255–2264	Jaguar	2001
	"Reproducing the Conformations of Protein-bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools" Bostrom, J., J. Comput.-Aided Mol. Des., 2001, 15, 1137-1152	MacroModel	2001
	"Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field" Reichert, D. E.; Norrby, P. O.; Welch, M. J., Inorg. Chem., 2001, 40, 5223-5230	MacroModel	2001
	"Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase" Keseru, G. M.; Kolossvary, I., J. Am. Chem. Soc., 2001, 123, 12708-12709	MacroModel	2001
	"Hessian-Free Low-Mode Conformational Search for Large-Scale Protein Loop Optimization: Application to c-jun N-Terminal Kinase JNK3" Kolossvary, I.; Keseru, G. M., J. Comp. Chem., 2001, 22, 21-30	MacroModel	2001
	"Novel Agouti-Related-Protein-Based Melanocortin-1 Receptor Antagonist" Thirumoorthy, R.; Holder, J. R.; Bauzo, R. M.; Richards, N. G. J.; Edison, A. S.; Haskell-Luevano, C., J. Med. Chem., 2001, 44, 4114-4124	MacroModel	2001
	"A Comparison of Methods for Pharmacophore Generation with the Catalyst Software and their Use for 3D-QSAR: Application to a Set of 4-aminopyridine Thrombin Inhibitors" Greenidge, P.A; Weiser, J., Mini Rev. Med. Chem., 2001, 1, 79-87	MacroModel	2001
	"Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations" Zhang, L.Y.; Gallicchio, E.; Friesner, R.A.; Levy, R.M., J. Comput. Chem., 2001, 22, 591–607	Glide	2001
	"New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model" Zhou, R.; Friesner, R. A.; Ghosh, A.; Rizzo, R. C.; Jorgensen, W. L.; Levy, R. M., J. Phys. Chem. B, 2001, 105, 10388–10397		2001
ö	"Activation of the C-H bond of Methane by Intermediate Q of Methane Monoozygenase: A Theoretical Study" Gherman, B. F.; Dunietz, B. D.; Whittington, D. A.; Lippard, S. J.; Friesner, R. A., J. Am. Chem. Soc., 2001, 123, 3836–3837	Jaguar	2001