Below are selected publications from all recent years; please check here to cite the use of Desmond

• •  ö  Wang, L.; Deng, Y.; Knight, J.L.; Wu, Y.; Kim, B.; Sherman, W.; Shelley, J.C.; Lin, T.; Abel, R., "Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors," J. Chem. Theory Comput., 2013, 9, 1282-1293
• •  ö  Liu, M.; Bender, S.A.; Cuny, G.D.; Sherman, W.; Glicksman, M.; Ray, S.S., "Type II Kinase Inhibitors Show an Unexpected Inhibition Mode against Parkinson’s Disease-Linked LRRK2 Mutant G2019S," Biochemistry, 2013, 52, 1725-1736
• •  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  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  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  Newman, A.H.; Beuming, T.; Banala, A.K.; Donthamsetti, P.; Pongetti, K.; LaBounty, A.; Levy, B.; Cao, J.; Michino, M.; Luedtke, R.P.; Javitch, J.A.; Shi, L., "Molecular determinants of selectivity and efficacy at the dopamine D3 receptor," J. Med. Chem., 2012, 55 (15), 6689–6699
• •  Hanoian, P.; Hammes-Schiffer S., "Water in the active site of ketosteroid isomerase," Biochemistry., 2011, 50, 6689-6700
• •  ö  Shivakumar, D.; Williams, J.; Wu, Y.; Damm, W.; Shelley, J.; Sherman, W., "Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field," J. Chem. Theory Comput., 2010, 6, 1509–1519
• •  ö  Guo, Z.; Mohanty, U.; Noehre, J.; Sawyer, T. K.; Sherman, W.; Krilov, G., "Probing the α-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis," Chem. Biol. Drug Des., 2010, 75, 348-359
• •  ö  Lyman, E.; Higgs, C.; Kim, B.; Lupyan, D.; Shelley, J. C.; Farid, R.; Voth, G. A., "A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A_2A Adenosine Receptor," Structure, 2009, 17, 1660-1668
• •  Shan, Y.; Seeliger, M. A.; Eastwood, M.P.; Frank, F.; Xu, H.; Jensen, M.; Dror, R.O.; Kuriyan, J.; and Shaw, D. E., "A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase," Proc. Natl. Acad. Sci. USA, 2009, 106, 139-144
• •  Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw, "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters," Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, 2006, November 11-17

• ö indicates papers (co)authored by Schrödinger scientist(s).