Citations

BioLuminate^®

• Zhu, K.; Day, T.; Warshaviak, D.; Murrett, C.; Friesner, R.; Pearlman, D., "Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction," Proteins, 2014, 82(8), 1646-1655
• Salam, N.K.; Adzhigirey, M.; Sherman, W.; Pearlman, D.A., "Structure-based approach to the prediction of disulfide bonds in proteins," Protein Eng Des Sel, 2014, 27(10), 365-74
• Beard, H.; Cholleti, A.; Pearlman, D.; Sherman, W.; Loving, K.A., "Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes," PLoS ONE, 2013, 8(12), e82849

Canvas

• 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
• 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

• 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

• 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

• • 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

• 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

• 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
• 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

• • Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J.Y.; Wang, L.; Lupyan, D.; Dahlgren, M.K.; Knight, J.L.; Kaus, J.W.; Cerutti, D.S.; Krilov, G.; Jorgensen, W.L.; Abel, R.; Friesner, R.A., "OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins," J. Chem. Theory Comput., 2015, DOI: 10.1021/acs.jctc.5b00864
  • 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

FEP+

• Chen, W.; Cui, D.; Jerome, S.; Michino, M.; Lenselink, E.; Huggins, D.; Beautrait, A.; Vendome, A.; Abel, R.; Friesner, R.A.; and Wang, L., "Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations". J. Chem. Inf. Model. 2023, 63 (10), 3171–3185
• Abel, R.; Wang, L.; Harder, E.D.; Berne, B.J.; Friesner, R.A., "Advancing Drug Discovery through Enhanced Free Energy Calculations," Acc. Chem. Res., 2017 50 (7), 1625-1632
• Kuhn, B.; Tichý, M.; Wang, L.; Robinson, S.; Martin, R.E.; Kuglstatter, A.; Benz, J.; Giroud, M., Schirmeister, T.; Abel, R.; Diederich, F.; Hert, J., "Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors," J. Med. Chem., 2017, 60 (6), 2485-2497
• Yu, H.S.; Deng, Y.; Wu, Y.; Sindhikara, D.; Rask, A.R.; Kimura, T.; Abel, R.; Wang, L., "Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets," J. Chem Theory Comput., 2017, 13 (12), 6290-6300
• Wang, L.; Deng, Y.; Wu, Y.; Kim, B.; LeBard, D.N.; Wandschneider, D.; Beachy, M.; Friesner, R.A; Abel, R., "Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery," J. Chem Theory Comput., 2017, 13 (1), 42-54
• Harder, E. et al., "OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins," J. Chem. Theory Comput., 2016, 12(1), 281–296
• Wang, L. et al., "Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field," J. Am. Chem. Soc., 2015, 137(7), 2695–2703

Glide

• 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
• 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.; 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

• 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
• 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

Jaguar

• Bochevarov, A.D.; Harder, E.; Hughes, T.F.; Greenwood, J.R.; Braden, D.A.; Philipp, D.M.; Rinaldo, D.; Halls, M.D.; Zhang, J.; Friesner, R.A., "Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences," Int. J. Quantum Chem., 2013, 113(18), 2110-2142

Jaguar pKa

• Bochevarov, A. D.; Watson, M. A.; Greenwood, J. R.; Philipp, D. M., "Multiconformation, density functional theory-based pKa prediction in application to large, flexible organic molecules with diverse functional groups," J. Chem. Theory Comput., 2016, 12(12), 6001–6019
• Yu, H. S.; Watson, M. A.; Bochevarov, A. D., "A Weighted Averaging Scheme and a Local Atomic Descriptor for pKa Prediction Based on Density Functional Theory," J. Chem. Inf. Mod., 2018, 58, 271–286
• Klicić, J. J.; Friesner, R. A.; Liu, S.-Y.; Guida, W. C., "Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods," J. Phys. Chem. A, 2002, 106, 1327–1335

LigPrep

LiveDesign

MacroModel

Maestro

Materials Science Suite

MS Combi

MS Jaguar

Phase

• 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

PIPER

• Chuang, G-Y.; Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S., "DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking," Biophys. J., 2008, 95, 4217-4227
• Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S., "PIPER: An FFT-based protein docking program with pairwise potentials," Proteins, 2006, 65, 392-406

Prime

• 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: Structure, Function and Bioinformatics, 2004, 55, 351-367
• Jacobson, M. P.; 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

• 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, 534-538

Protein Preparation Wizard

• Sastry, G.M.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W., "Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments," J. Comput. Aid. Mol. Des., 2013, 27(3), 221-234

PyMOL

QikProp

QM-Polarized Ligand Docking

• 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

• 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

Semiempirical NDDO

Shape Screening

• Sastry, G.M.; Dixon, S.L.; Sherman, W., "Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring," J. Chem. Inf. Model., 2011, 51, 2455-2466

SiteMap

• Halgren, T., "Identifying and characterizing binding sites and assessing druggability," J. Chem. Inf. Model., 2009, 49, 377–389
• Halgren, T., "New method for fast and accurate binding-site identification and analysis," Chem. Biol. Drug Des., 2007, 69, 146–148

WaterMap

• Abel, R.; Young, T.; Farid, R.; Berne, B.J.; Friesner, R.A., "The role of the active site solvent in the thermodynamics of factor Xa-ligand binding" J. Am. Chem. Soc., 2008, 130(9), 2817–2831
• Young, T.; Abel, R.; Kim, B.; Berne, B.J.; Friesner, R.A., "Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding" Proc. Natl. Acad. Sci. U S A.,, 2007, 104, 808-813