Thank you for using Schrödinger software in your research. When preparing a manuscript, please use the citations below to cite each program.

Canvas

• •  ö  Duan, J.; Dixon, S.L.; Lowrie, J.F.; Sherman, W., "Analysis and Comparison of 2D Fingerprints: Insights into Database Screening Performance Using Eight Fingerprint Methods," J. Molec. Graph. Model., 2010, 29, 157-170
• •  ö  Sastry, M.; Lowrie, J.F.; Dixon, S.L.; Sherman, W., "Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments," J. Chem. Inf. Model., 2010, 50, 771–784

CombiGlide

ConfGen

• •  ö  Watts, K.S.; Dalal, P.; Murphy, R.B.; Sherman, W.; Friesner, R.A.; Shelley, J.C., "ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers," J.Chem. Inf. Model., 2010, 50, 534-546

Core Hopping

Desmond

• •  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
• •  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

e-Pharmacophores

• •  ö  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
• •  ö  Loving, K.; Salam, N. K.; Sherman, W, "Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation," J. Comput. Aided Mol. Des., 2009, 23, 541–554

Epik

• •  ö  Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C., "Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution," J. Comput. Aided Mol. Des., 2010, 24, 591-604
• •  ö  Shelley, J.C.; Cholleti, A.; Frye, L; Greenwood, J.R.; Timlin, M.R.; Uchimaya, M., "Epik: a software program for pK_a prediction and protonation state generation for drug-like molecules," J. Comp.-Aided Mol. Design, 2007, 21, 681-691

Force Fields

• •  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
• •  Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives, J., "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids," J. Am. Chem. Soc., 1996, 118 (45), 11225-11236
• •  Jorgensen, W.L.; Tirado-Rives, J., "The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin," J. Am. Chem. Soc., 1988, 110(6), 1657-1666

Glide

• •  ö  Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren,T. A.; Sanschagrin, P. C.; Mainz, D. T., "Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes," J. Med. Chem., 2006, 49, 6177–6196
• •  ö  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
• •  ö  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

Induced Fit

• •  ö  Farid, R.; Day, T.; Friesner, R. A.; Pearlstein, R. A., "New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies," Bioorg. & Med. Chem., 2006, 14, 3160-3173
• •  ö  Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R., "Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects," J. Med. Chem., 2006, 49, 534-553
• •  ö  Sherman, W.; Beard, H. S.; Farid, R., "Use of an Induced Fit Receptor Structure in Virtual Screening," Chemical Biology & Drug Design, 2006, 67, 83-84

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