Methods Development
• ö Osguthorpe, D.J.; Sherman, W.; Hagler, A.T., "Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering," Chem. Biol. Drug Des.,, 2012, 80(2), 182-193
• ö Bell, J.A., Cao, Y., Gunn, J.R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R., "PrimeX and the Schrödinger Computational Chemistry Suite of Programs," International Tables for Crystallography, 2012, F(18), 534-538
• ö Osguthorpe D.J.; Sherman, W.; Hagler, A.T., "Exploring protein flexibility: Incorporating structural ensembles from crystal structures and simulation into virtual screening protocols," J. Phys. Chem. B, 2012, 116(23), 6952-6959
• ö Hughes, T. F.; Harvey, J. N.; Friesner, R. A., "A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation," Phys. Chem, 2012, 14, 7724-7738
• ö Shivakumar, D.; Harder, E; Damm, W.; Friesner, R.A.; Sherman, W., "Improving the prediction of absolute solvation free energies using the Next Generation OPLS force field," J. Chem. Theory Comput., 2012, 8(8), 2553-2558
• ö Leung, S.S.F.; Mijalkovic, J.; Borrelli, K.; Jacobson, M.P., "Testing Physical Models of Passive Membrane Permeation," J. Chem. Inf. Model., 2012, 52(6), 1621-1636
Applications
• ö Tran, Q.T.; Williams, S.; Farid, R.; Erdemli, G.; Pearlstein, R., "The translocation kinetics of antibiotics through porin OmpC: Insights from structure-based solvation mapping using watermap ," Proteins, 2013, 81(2), 291-299
• ö Myrianthopoulos, V.; Kritsanida, M.; Gaboriaud-Kolar, N.; Magiatis, P.; Ferandin, Y.; Durieu, E.; Lozach, O.; Cappel, D.; Soundararajan M; Filippakopoulos P; Sherman W; Knapp S; Meijer L; Mikros E; Skaltsounis AL, "Novel inverse binding mode of indirubin derivatives yields improved selectivity for DYRK kinases," ACS Med Chem Lett, 2013, 4(1), 22-26
• Galstyan, A.; Robertazzi, A.; Knapp, E.W., "Oxygen-Evolving Mn Cluster in Photosystem II: The Protonation Pattern and Oxidation State in the High-Resolution Crystal Structure," J. Am. Chem. Soc, 2012, 134, 7442–7449
• Lousada, M.C.; Johansson, A.J.; Brinck, T.; Jonsson, M., "Mechanism of H2O2 Decomposition on Transition Metal Oxide Surfaces," J. Phys. Chem. C., 2012, 116, 9533–9543
• Coletti, C.; Gonsalvi, L.; Guerriero, A.; Marvelli, L.; Peruzzini, M.; Reginato, G.; Re, N., "Electron-Poor Rhenium Allenylidenes and Their Reactivity toward Phosphines: A Combined Experimental and Theoretical Study," Organometallics., 2012, 31, 57–69
• Lavecchia, A.; Di Giovanni, C.; Pesapane, A.; Montuori, N.; Ragno, P.; Martucci, N.M.; Masullo, M.; De Vendittis, E.; Novellino, E., "Discovery of New Inhibitors of Cdc25B Dual Specificity Phosphatases by Structure-Based Virtual Screening," J. Med. Chem., 2012, 55, 4142–4158
• ö Per Plenge, Lei Shi, Thijs Beuming, Jerez Te, Amy Hauck Newman, Harel Weinstein, Ulrik Gether and Claus J. Loland, "Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter," J. Biol. Chem., 2012, 287, 39316-39326
• Fu, J.; Si, P.; Zheng, M.; Chen, L.; Shen, X.; Tang, Y.; Li, W., "Discovery of new non-steroidal FXR ligands via a virtual screening workflow based on Phase shape and induced fit docking," Bioorg. Med. Chem. Lett., 2012, 22(22), 6848-6853
• Gemma, S.; Camodeca, C.; Coccone, S.S.; Joshi, B.P.; Bernetti, M.; Moretti, V.; Brogi S.; de Marcos, M.C.B.; Savini, L.; Taramelli, D.; Basilico, N.; Parapini, S.; Rottmann, M.; Brun, R.; Lamponi, S.; Caccia, S.; Guiso, G.; Summers, R.L.; Martin, R.E.; S, "Optimization of 4-aminoquinoline/clotrimazole-Based Hybrid antimalarials: Further structure–activity relationships, in vivo studies, and preliminary toxicity profiling," J. Med. Chem., 2012, 55(15), 6948-6967