Some recent publications include:

• Cho, A. E.; Guallar, V.; Berne, B.; Friesner, R. A., "Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach", J. Comput. Chem. 2005, 26, 915-931.
• Krovat, E. M.; Steindl, T.; Langer, T., "Recent Advances in Docking and Scoring", Current Computer-Aided Drug Design, 2005, 1, 93-102.
• Kontoyianni, M; Sokol, GS; McClellan, LM., "Evaluation of library ranking efficacy in virtual screening", J. Comput. Chem. 2005, 26, 11-22.
• Kirkpatrick, P., "Virtual screening: Gliding to success", Nature Reviews Drug Discovery 2004, 3, 299.
• Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L., "Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening", J. Med. Chem. 2004, 47, 1750-1759.
• Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.; Shenkin, P. S, "Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy", J. Med. Chem. 2004, 47, 1739-1749.
• Klon, A. E.; Glick, M.; Davies, J. W., "Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease", J. Chem. Inf. Comput. Sci., 2004, 44, 2216-2224.
• Ruddat, V. C.; Mogul, R.; Chorny, I.; Chen, C.; Perrin, N.; Whitman, S.; Kenyon, V.; Jacobson, M. P.; Bernasconi, C. F.; Holman, T. R., "Tryptophan 500 and Arginine 707 Define Product and Substrate Active Site Binding in Soybean Lipoxygenase-1", Biochemistry, 2004, 43,13063-13071.
• Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D., "Comparative evaluation of eight docking tools for docking and virtual screening accuracy", Proteins. 2004, 57, 225-242.
• Perola, E.; Walters, W.P.; Charifson, P.S., "A Detailed Comparison of Current Docking and Scoring Methods on Systems of Pharmaceutical Relevance", Proteins, 2004, 56, 235-249.
• Klon, A. E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J. W., "Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results", J. Med. Chem. 2004, 47, 2743-2749.
• Bytheway, I.; Cochran, S., "Validation of Molecular Docking Calculations Involving FGF-1 and FGF-2", J. Med. Chem. 2004, 47, 1683-1693.
• Kontoyianni, M.; McClellan, L. M.; Sokol, G. S., "Evaluation of Docking Performance: Comparative Data on Docking Algorithms", J. Med. Chem. 2004, 47, 558-565.
• Schulz-Gasch, T; Stahl, M., "Binding site characteristics in structure-based virtual screening: evaluation of current docking tools", J. Mol. Mod. 2003, 9, 47-57.
• Wu, T. Y. H.; Wagner, K. W.; Bursulaya, B.; Schultz, P. G.; Deveraux, Q. L. "Development and Characterization of Nonpeptidic Small Molecule Inhibitors of the XIAP/Caspase-3 Interaction", Chemistry & Biology 2003, 10, 759-767.
• Kuo, G.-H.; Prouty, C.; DeAngelis, A.; Shen, L.; O'Neill, D. J.; Shah, C.; Connolly, P. J.; Murray, W. V.; Conway, B. R.; Cheung, P.; Westover, L.; Xu, J. Z.; Look, R. A.; Demarest, K. T.; Emanuel, S.; Middleton, S. A.; Jolliffe, L.; Beavers, M. P.; Chen, X. "Synthesis and Discovery of Macrocyclic Polyoxygenated Bis-7-azaindolylmaleimides as a Novel Series of Potent and Highly Selective Glycogen Synthase Kinase-3 Inhibitors", J. Med. Chem. 2003, 46, 4021-4031.
• Nilsson, J. W.; Kvarnstrom, I.; Musil, D.; Nilsson, I.; Samulesson, B. "Synthesis and SAR of Thrombin Inhibitors Incorporating a Novel 4-Amino-Morpholinone Scaffold: Analysis of X-ray Crystal Structure of Enzyme Inhibitor Complex", J. Med. Chem. 2003, 46, 3985-4001.
• Bjerrum, E. J.; Kristensen, A. S.; Pickering, D. S.; Greenwood, J. R.; Nielsen, B.; Liljefors, T.; Schousboe, A.; Brauner-Osborne, H.; Madsen, U. "Design, Synthesis, and Pharmacology of a Highly Subtype-Selective GluR1/2 Agonist, (RS)-2-Amino-3-(4-chloro-3-hydroxy-5-isoxazolyl)propionic Acid (Cl-HIBO)", J. Med. Chem. 2003, 46, 2246-2249. 
• Brehm, L.; Greenwood, J. R.; Hansen, K. B.; Nielsen, B.; Egebjerg, J.; Stensbol, T. B.; Brauner-Osborne, H.; Slok, F. A.; Kronborg, T. T. A.; Krogsgaard-Larsen, P. "(S)-2-Amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl) propionic Acid, a Potent and Selective Agonist at the GluR5 Subtype of Ionotropic Glutamate Receptors. Synthesis, Modeling, and Molecular Pharmacology", J. Med. Chem. 2003, 46, 1350-1358. 
• Thorstensson, F.; Kvarnstrom, I.; Musil, D.; Nilsson, I.; Samuelsson, B. "Synthesis of Novel Thrombin Inhibitors. Use of Ring-Closing Metathesis Reactions for Synthesis of P2 Cyclopentene- and Cyclohexenedicarboxylic Acid Derivatives", J. Med. Chem. 2003, 46, 1165-1179. 
• Bunch, L.; Liljefors, T.; Greenwood, J. R.; Frydenvang, K.; Brauner-Osborne, H.; Krogsgaard-Larsen, P.; Madsen, U. "Rational Design, Synthesis, and Pharmacological Evaluation of 2-Azanorbornane-3-exo,5-endo-dicarboxylic Acid: A Novel Conformationally Restricted Glutamic Acid Analogue", J. Org. Chem. 2003, 68, 1489-1495. 
• Johansen, T. N.; Greenwood, J. R.; Frydenvang, K.; Madsen, U.; Krogsgaard-Larsen, P. "Stereostructure-Activity Studies on Agonists at the AMPA and Kainate Subtypes of Ionotropic Glutamate Receptors", Chirality 2003, 15, 167-179.
• Neamati, N.; Lin, Z.; Karki, R. G.; Orr, A.; Cowansage, K.; Strumberg, D.; Pais, G. C. G.; Voigt, J. H.; Nicklaus, M. C.; Winslow, H. E.; Zhao, H.; Turpin, J. A.; Yi, J.; Skalka, A. M.; Burke, T. R., Jr.; Pommier, Y. "Metal-Dependent Inhibition of HIV-1 Integrase", J. Med. Chem. 2002, 45, 5661-5670. 
• Clausen, R. P.; Brauner-Osborne, H.; Greenwood, J. R.; Hermit, M. B.; Stensbol, T. B.; Nielsen, B.; Krogsgaard-Larsen, P. "Selective Agonists at Group II Metabotropic Glutamate Receptors: Synthesis, Stereochemistry, and Molecular Pharmacology of (S)- and (R)-2-Amino-4-(4-hydroxy[1,2,5]thiadiazol-3-yl) butyric Acid", J. Med. Chem. 2002, 45, 4240-4245. 
• Zhang, L., E. Gallicchio, R. Friesner, and R.M. Levy, "Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations," J. Comp. Chem. 2001, 22, 591-607.
• Zhou R., Friesner R. A., Ghosh A., Rizzo R. C., Jorgensen W. L., Levy R. M., "New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model" J. Phys. Chem. B 2001,105, 10388-10397.