Below are recent publications that highlight the use or development of Schrodinger software:
Benltifa, M.; Hayes, J. M.; Vidal, S.; Gueyrard, D.; Goekjian, P. G.; Praly, J.; Kizilis, G.; Tiraidis, C.; Alexacou, K.; Chrysina, E. D.; Zographos, S. E.; Leonidas, D. D.; Archontis, G.; Oikonomakos, N. G., "Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitors," Bioorg. Med. Chem., 2009, 17, 7368-7380. Link
Bowers, A.A.; Greshock, T.J.; West, N.; Estiu, G.; Schreiber, S.L.; Wiest, O.; Williams, R.M.; Bradner, J.E., "Synthesis and Conformation-Activity Relationships of the Peptide Isosteres of FK228 and Largazole," J. Amer. Chem. Soc., 2009, 131, 2900-2905. Link
Chen, I.J.; Hubbard, R.E., "Lessons for fragment library design: analysis of output from multiple screening campaigns," J. Comput.-Aided Mol. Des., 2009, 23, 603-620. Link
Cho, A. E.; Rinaldo, D., "Extension of QM/MM docking and its applications to metalloproteins," J. Comput. Chem., 2009, 30, 2609-2616. Link
Chung, J. Y.; Hah, J.; Cho, A. E., "Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites," J. Chem. Inf. Model., 2009, 49, 2382-2387. Link
Das, D.; Koh, Y.; Tojo, Y.; Ghosh, A.K.; Mitsuya, H., "Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model," J. Chem. Inf. Model., 2009 [ASAP]. Link
Dror, R.O.; Arlow, D.H.; Borhani, D.W.; Jensen, M.O.; Piana, S.; Shaw, D.E., "Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations," Proc. Natl. Acad. Sci. USA, 2009, 106, 4689-4694. Link
King, A.R.; Dotsey, E.Y.; Lodola, A.; Jung, K.M.; Ghomian, A.; Qiu, Y.; Fu, J.; Mor, M.; Piomelli, D., "Discovery of Potent and Reversible Monoacylglycerol Lipase Inhibitors," Chem. Biol., 2009, 16, 1045-1052. Link
Miller, K.J.; Wu, G.Y.; Varnes, J.G.; Levesque, P.; Li, J.L.; Li, D.S.; Robl, J.A.; Rossi, K.A.; Wacker, D.A., "Position 5.46 of the Serotonin 5-HT2A Receptor Contributes to a Species-Dependent Variation for the 5-HT2C Agonist (R)-9-Ethyl-1,3,4,10b-tetrahydro-7-trifluoromethylpyrazino[2,1-a]isoindol-6(2H)-one: Impact on Selectivity and Toxicological Evaluation," Mol. Pharmacol., 2009, 76, 1211-1219. Link
Park, Y.S.; Widawsky, J.R.; Kamenetska, M.; Steigerwald, M.L.; Hybertsen, M.S.; Nuckolls, C.; Venkataraman, L.,"Frustrated Rotations in Single-Molecule Junctions," J. Amer. Chem. Soc., 2009, 131, 10820-10821. Link
Salam, N. K.; Nuti, R.; Sherman, W., "Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis," J. Chem. Inf. Model., 2009, 49, 2356-2368. Link
Tian, L.; Friesner, R.A., "QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism," J. Chem. Theory Comput., 2009, 5, 1421-1431. Link
Zhong, H.; Trana, L.M.; Stang, J.L., "Induced-fit docking studies of the active and inactive states of protein tyrosine kinases," J. Mol. Graph. Model., 2009, 28, 336-346. Link
Maestro Cover Graphics
Here are two recent publications that used Maestro to create their journal cover graphic:
Nichols, S.E.; Domaoal, R. A.; Thakur, V.V.; Tirado-Rives, J.; Anderson, K.S.; Jorgensen, W.L., "Discovery of Wild-Type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures," J. Chem. Inf. Model., 2009, 49, 1272-1279. Link
Williamson, D.S.; Borgognoni, J.; Clay, A.; Daniels, Z.; Dokurno, P.; Foloppe, N.; Francis, G.L.; Graham, C.J.; Howes, R.; Macias, A.T.; Murray, J.B.; Parson, R.; Shaw, T.; Surgenor, A.E.; Terry, L.; Wang, Y.; Wood, M.; Massey, A.J. "Novel Adenosine-Derived Inhibitors of 70 kDa Heat Shock Protein, Discovered Through Structure-Based Design," J. Med. Chem., 2009, 52, 1510-1513. Link