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

Canvas

Canvas, version 1.4, Schrödinger, LLC, New York, NY, 2011.

Sastry, M.; Lowrie, J. F.; Dixon, S. L.; and Sherman, W. "Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments," J. Chem. Inf. Model., 2010, 50, 771.

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.

CombiGlide

CombiGlide, version 2.7, Schrödinger, LLC, New York, NY, 2011.

ConfGen

ConfGen, version 2.3, Schrödinger, LLC, New York, NY, 2011.

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.

Chen, I.; Foloppe, N.; "Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst," J.Chem. Inf. Model., 2010, 50, 822-839.

Core Hopping

Core Hopping, version 1.1, Schrödinger, LLC, New York, NY, 2011.

Desmond

Desmond Molecular Dynamics System, version 3.0, D. E. Shaw Research, New York, NY, 2011. Maestro-Desmond Interoperability Tools, version 3.0, Schrödinger, New York, NY, 2011.

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, November 11-17, 2006.

Shivakumar, D.; Williams, J.; Wu, Y.; Damm, W.; Shelley, J.; Sherman, W., "Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation andt he OPLS Force Field," J. Chem. Theory. Comput., 201, 6(5), 1509-1519.

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 (4), 348-359.

Epik

Epik, version 2.2, Schrödinger, LLC, New York, NY, 2011.

Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin M. R.; Uchiyama, M. "Epik: a software program for pKa prediction and protonation state generation for druglike molecules," J. Comput. Aided Mol. Des., 2007, 21, 681–691.

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.

Park, M.; Gao, C.; Stern, H.A., "Estimating binding affinities by docking/scoring methods using variable protonation states," Proteins, 2011, 79, 304-314.

Please note that the pKa and tautomeric databases provided with Epik are copyrighted material, and should not be extracted, reproduced, or used outside of the context of Epik or LigPrep licensed calculations.

Glide

Glide, version 5.7, Schrödinger, LLC, New York, NY, 2011.

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.

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.

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.

Park, M.; Gao, C.; Stern, H.A., "Estimating binding affinities by docking/scoring methods using variable protonation states," Proteins, 2011, 79, 304-314.

Induced Fit

Schrödinger Suite 2011 Induced Fit Docking protocol; Glide version 5.7, Schrödinger, LLC, New York, NY, 2011; Prime version 3.0, Schrödinger, LLC, New York, NY, 2011.

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.

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.

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.

Jaguar

Jaguar, version 7.8, Schrödinger, LLC, New York, NY, 2011.

Liaison

Liaison, version 5.7, Schrödinger, LLC, New York, NY, 2011; Strike, version 2.0, Schrödinger, LLC, New York, NY, 2011.

Ligand & Structure-Based Descriptors

Schrödinger Suite 2011 Ligand and Structure-Based Descriptors protocol; Liaison version 5.7, Schrödinger, LLC, New York, NY, 2011; MacroModel version 9.9, Schrödinger, LLC, New York, NY, 2011; Prime version 3.0, Schrödinger, LLC, New York, NY, 2011; QikProp version 3.4, Schrödinger, LLC, New York, NY, 2011.

LigPrep

LigPrep, version 2.5, Schrödinger, LLC, New York, NY, 2011.

MacroModel

MacroModel, version 9.9, Schrödinger, LLC, New York, NY, 2011.

Maestro

Maestro, version 9.2, Schrödinger, LLC, New York, NY, 2011.

Phase

Phase, version 3.3, Schrödinger, LLC, New York, NY, 2011.

Dixon, S. L.; Smondyrev, A. M.; Knoll, E. H.; Rao, S. N.; Shaw, D. E.; Friesner, R. A., "PHASE: A New Engine for Pharmacophore Perception, 3D QSAR Model Development, and 3D Database Screening. 1. Methodology and Preliminary Results," J. Comput. Aided Mol. Des., 2006, 20, 647-671.

Dixon, S. L.; Smondyrev, A. M.; Rao, S. N., "PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching," Chem. Biol. Drug Des., 2006, 67, 370-372.

Prime

Prime, version 3.0, Schrödinger, LLC, New York, NY, 2011.

Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J. F.; Honig, B.; Shaw, D. E.; Friesner, R. A., "A Hierarchical Approach to All-Atom Protein Loop Prediction," Proteins, 2004, 55, 351-367.

Jacobson, M. P.; R. A. Friesner, R.A.; Xiang, Z.; Honig, B., "On the Role of Crystal Packing Forces in Determining Protein Sidechain Conformations," J. Mol. Biol., 2002, 320, 597-608.

PrimeX

PrimeX, version 1.8, Schrödinger, LLC, New York, NY, 2011.

Arnold, E.; Himmel, D.M.; Rossmann, M.G. ed., International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules, 2nd edition, Chichester: John Wiley and Sons, in press.

Protein Preparation Wizard

Schrödinger Suite 2011 Protein Preparation Wizard; Epik version 2.2, Schrödinger, LLC, New York, NY, 2011; Impact version 5.7, Schrödinger, LLC, New York, NY, 2011; Prime version 3.0, Schrödinger, LLC, New York, NY, 2011. 

QikProp

QikProp, version 3.4, Schrödinger, LLC, New York, NY, 2011.

QM-Polarized Ligand Docking

Schrödinger Suite 2011 QM-Polarized Ligand Docking protocol; Glide version 5.7, Schrödinger, LLC, New York, NY, 2011; Jaguar version 7.8, Schrödinger, LLC, New York, NY, 2011; QSite version 5.7, Schrödinger, LLC, New York, NY, 2011.

Cho, A. E.; Guallar, V.; Berne, B.; Friesner, R. A., "Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach," J. Comput. Chem., 2005, 26, 915-931.

QSite

QSite, version 5.7, Schrödinger, LLC, New York, NY, 2011.

Murphy, R. B.; Philipp, D. M.; Friesner, R. A., "A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments," J. Comp. Chem., 2000, 21, 1442-1457.

Philipp, D. M.; Friesner, R. A., "Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide," J. Comp. Chem., 1999, 20, 1468-1494.

SiteMap

SiteMap, version 2.5, Schrödinger, LLC, New York, NY, 2011.

Halgren, T., "New Method for Fast and Accurate Binding-site Identification and Analysis," Chem. Biol. Drug Des., 2007, 69, 146–148.

Halgren, T., "Identifying and Characterizing Binding Sites and Assessing Druggability," J. Chem. Inf. Model., 2009, 49, 377–389.

Strike

Strike, version 2.0, Schrödinger, LLC, New York, NY, 2011.