Schrodinger Suite
- provides accurate, reliable, and high performance computational technology to solve real-world problems in life science research.
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Citations
CANVAS: Sastry et al. Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments. J. Chem. Inf. Model. 2010, 50:771. Duan et al. Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods. J. Molec. Graph. Model., 2010. 29:157-170.
ConfGen: Watts et al. ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. J.Chem. Inf. Model. 2010. 50:534-546. Chen and Foloppe. 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.
Desmond: Bowers et al. 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 et al. 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. Guo et al. Probing the α-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis. Chem Biol. Drug Des. 2010. 75:348-359.
Epik: Shelley et al. Epik: a software program for pKa prediction and protonation state generation for druglike molecules. J. Comput. Aided Mol. Des. 2007. 21:681–691. Greenwood et al. 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 et al. Estimating binding affinities by docking/scoring methods using variable protonation states. Proteins. 2010. 79(1):304-314.
Glide: Friesner et al. 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 et al. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening. J. Med. Chem. 2004. 47:1750–1759. Friesner et al. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes. J. Med. Chem. 2006. 49:6177–6196.
Induced Fit: Sherman et al. Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects. J. Med. Chem. 2006. 49:534-554. Sherman et al. Use of an Induced Fit Receptor Structure in Virtual Screening. Chem. Biol. Drug Des. 2006. 67:83-84.
Phase:
Dixon et al. 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 et al. PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching. Chem. Biol. Drug Des. 2006. 67:370-372.
Prime: Jacobson et al. A Hierarchical Approach to All-Atom Protein Loop Prediction. Proteins. 2004. 55:351-367. Jacobson et al. On the Role of Crystal Packing Forces in Determining Protein Sidechain Conformations. J. Mol. Biol. 2002. 320:597-608.
PrimeX:
Arnold et al. ed. International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules, 2nd edition, Chichester: John Wiley and Sons, in press.
QM-Polarized Ligand Docking: Cho et al. Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach. J. Comput. Chem. 2005. 26:915-931.
QSite: Murphy et al. 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 and Friesner. Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. J. Comp. Chem. 1999. 20:1468-1494.
SiteMap: Halgren. Identifying and Characterizing Binding Sites and Assessing Druggability. J. Chem. Inf. Model. 2009. 49:377–389. Halgren. "New Method for Fast and Accurate Binding-site Identification and Analysis. Chem. Biol. Drug Des. 2007. 69:146–148.
Technical Notes
The SBGrid Consortium has a license for a limited number of seats for the Schrodinger Molecular Modeling Suite. Licensed applications include Glide, Liaison, Qsite, Jaguar, pKa, MacroModel, ConfGen, QikProp, Prime, LigPrep, Phase, Strike, CombiGlide, Epik, SiteMap, PrimeX, XP Visualizer, Canvas, Core Hopping, as well as access to KNIME and Maestro.
Due to its large size, the software is not in the default installation. Please email bugs@sbgrid.org to request installation for your site.
License Type
This software is distributed under a Commercial license.
