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

Schrödinger Release 2021-4: BioLuminate, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: Canvas, Schrödinger, LLC, New York, NY, 2021.

 


 

 

CombiGlide

Schrödinger Release 2021-4: CombiGlide, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: ConfGen, Schrödinger, LLC, New York, NY, 2021.

 


 

 

Core Hopping

Schrödinger Release 2021-4: Core Hopping, Schrödinger, LLC, New York, NY, 2021.

 


 

CovDock

  • Zhu, K.; Borrelli, K.W.; Greenwood, J.R.; Day, T.; Abel, R.; Farid, R.S.; Harder, E., "Docking covalent inhibitors: A parameter free approach to pose prediction and scoring," J. Chem. Inf. Model., 2014, 54, 1932−1940

 

 


 

 

Desmond

Schrödinger Release 2021-4: Desmond Molecular Dynamics System, D. E. Shaw Research, New York, NY, 2021. Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2021.

 


 

 

e-Pharmacophores

 


 

 

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 pKa prediction and protonation state generation for drug-like molecules," J. Comp.-Aided Mol. Design, 2007, 21, 681-691

Schrödinger Release 2021-4: Epik, Schrödinger, LLC, New York, NY, 2021.

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.

 


 

 

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+

Schrödinger Release 2021-4: FEP+, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: Glide, Schrödinger, LLC, New York, NY, 2021.

 


 

 

Induced Fit

Schrödinger Release 2021-4: Induced Fit Docking protocol; Glide, Schrödinger, LLC, New York, NY, 2021; Prime, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: Jaguar, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: Jaguar pKa, Schrödinger, LLC, New York, NY, 2021.

 


 

 

LigPrep

Schrödinger Release 2021-4: LigPrep, Schrödinger, LLC, New York, NY, 2021.

 


 

 

MacroModel

Schrödinger Release 2021-4: MacroModel, Schrödinger, LLC, New York, NY, 2021.

 


 

 

Maestro

Schrödinger Release 2021-4: Maestro, Schrödinger, LLC, New York, NY, 2021.

 


 

 

MS Combi

Schrödinger Release 2021-4: MS Combi, Schrödinger, LLC, New York, NY, 2021.

 


 

 

MS Jaguar

Schrödinger Release 2021-4: MS Jaguar, Schrödinger, LLC, New York, NY, 2021.

 


 

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

Schrödinger Release  2021-4: Phase, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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
    1. http://structure.bu.edu/content/protein-protein-docking
    2. http://rosettadesigngroup.com/blog/535/capri-state-of-protein-protein-docking/
    3. http://www.ebi.ac.uk/msd-srv/capri/
  1. Fernández-Recio, J .; Sternberg, M.J.E., “The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona”, Proteins: Structure, Function and Bioinformatics, 2010, 78, 3065-3066. (http://onlinelibrary.wiley.com/doi/10.1002/prot.22801/abstract)

 


 

 

Prime

Schrödinger Release 2021-4: Prime, Schrödinger, LLC, New York, NY, 2021.

 


 

 

PrimeX

Schrödinger Release 2021-4: PrimeX, Schrödinger, LLC, New York, NY, 2021.

 


 

 

Protein Preparation Wizard

Schrödinger Release 2021-4: Protein Preparation Wizard; Epik,  Schrödinger, LLC, New York, NY, 2021; Impact, Schrödinger, LLC, New York, NY; Prime, Schrödinger, LLC, New York, NY, 2021.

 


 

 

PyMOL

For instructions on citing PyMOL, please visit www.pymol.org/citing.

 


 

 

QikProp

Schrödinger Release 2021-4: QikProp, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: QM-Polarized Ligand Docking protocol; Glide, Schrödinger, LLC, New York, NY, 2021; Jaguar, Schrödinger, LLC, New York, NY, 2021; QSite, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release 2021-4: QSite, Schrödinger, LLC, New York, NY, 2021.

 


 

 

Semiempirical NDDO

Schrödinger Release 2021-4: Semiempirical NDDO protocol; Jaguar, Schrödinger, LLC, New York, NY, 2021; MOPAC, Schrödinger, LLC, New York, NY, 2021.

 


 

 

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

Schrödinger Release  2021-4: Phase, Schrödinger, LLC, New York, NY, 2021.

 


 

 

SiteMap

Schrödinger Release 2021-4: SiteMap, Schrödinger, LLC, New York, NY, 2021.

 


 

 

WaterMap

Schrödinger Release 2021-4: WaterMap, Schrödinger, LLC, New York, NY, 2021.


 

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