Methods Development
• ö Bell, J.A.; Ho, K.L.; Farid, R., "Significant reduction in errors associated with non-bonded contacts in protein crystal structures: automated all-atom refinement with PrimeX," Acta Cryst. D, 2012, D68, 935-952
• ö An, Y.; Sherman, W.; Dixon, S.L., "Hole filling and library optimization: Application to commercially available fragment libraries," Bioorg. Med. Chem., 2012, 20, 5379–5387
• ö Repasky, M.P.; Murphy, R.B.; Banks, J.L.; Greenwood, J.R.; Tubert-Brohman, I.; Bhat, S.; Friesner, R.A., "Docking performance of the Glide program as evaluated on the Astex and DUD datasets: A complete set of Glide SP results and selected results for a new scoring function integrating WaterMap and Glide," J. Comput-Aided Mol. Des., 2012, 26, 787-799
• ö Sastry, G.M.; Dixon, S.L.; Sherman, W., "Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring," J. Chem. Inf. Model., 2011, 51, 2455-2466
• ö Zhao, S.; Zhu, K.; Li, J.; Friesner, R., "Progress in super long loop prediction ," Proteins, 2011, 79, 2920-2935
Applications
• Rafi, S.B.; Hearn, B.R.; Vedantham, P.; Jacobson, M.P.; Renslo, A.R., "Predicting and improving the membrane permeability of peptidic small molecules," J. Med. Chem., 2012, 55(7), 3163-3169
• ö Shah, F.; Jiri, G.; Legac, J.; Shivakumar, D.; Sherman, W.; Rosenthal, P.; Avery, M., "Computer-aided drug design of falcipain inhibitors: Virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis," J. Chem. Inf. Model., 2011, 52, 696-710
• ö Beuming, T.; Che, Y.; Abel, R.; Kim, B.; Shanmugasundaram, V.; Sherman, W., "Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization," Proteins, 2011, 80, 871-83
• ö Snyder. P.W.; Mecinovic, J.; Moustakas, D.; Thomas, S, III.; Harder, M.l.; Mack, E.; Lockett, M.; Héroux, A.; Sherman, W.; Whitesides, G., "Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase," PNAS, 2011, 108, 17889-17894
Perspective
• ö Huggins. D.J.; Sherman, W.; Tidor, Bruce., "Rational approaches to improving selectivity in drug design," J. Med. Chem., 2012, 55, 1424-1444