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

LigPrep

MacroModel

Maestro

Phase

• •  ö  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
• •  ö  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

Phase Shape

• •  ö  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

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

• •  ö  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
• •  ö  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

• •  ö  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

PyMOL

QikProp

QM-Polarized Ligand Docking

• •  ö  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

SiteMap

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

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