Below are recent publications highlighting the use of Schrödinger software.
Methods papers
Canvas Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments Madhavi Sastry‡, Jeffrey F. Lowrie†, Steven L. Dixon† and Woody Sherman Journal of Chemical Information and Modeling, ASAP Article http://pubs.acs.org/doi/abs/10.1021/ci100062n
ConfGen ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers K. Shawn Watts, Pranav Dalal, Robert B. Murphy, Woody Sherman, Rich A. Friesner, John C. Shelley Journal of Chemical Information and Modeling, ASAP Article http://dx.doi.org/10.1021/ci100015j
Fragment-based drug design Computational Approaches for Fragment-Based and De Novo Design Kathryn Loving, Ian Alberts, Woody Sherman Current Topics in Medicinal Chemistry 2010 10 (1), 14-32 http://dx.doi.org/10.2174/156802610790232305
Applications: Computer-aided drug design
WaterMap High-energy water sites determine peptide binding affinity and specificity of PDZ domains Thijs Beuming, Ramy Farid, Woody Sherman Protein Science 2009 18 (8), 1609-1619 http://dx.doi.org/10.1002/pro.177
WaterMap, Desmond, SiteMap, MacroModel, QSite The Glutamate Receptor GluR5 Agonist (S)-2-Amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)propionic Acid and the 8-Methyl Analogue: Synthesis, Molecular Pharmacology, and Biostructural Characterization Rasmus P. Clausen, Peter Naur, Anders S. Kristensen, Jeremy R. Greenwood, Mette Strange, Hans Brauner-Osborne, Anders A. Jensen, Anne Sophie T. Nielsen, Ulla Geneser, Lone M. Ringgaard, Birgitte Nielsen, Darryl S. Pickering, Lotte Brehm, Michael Gajhede, Povl Krogsgaard-Larsen, Jette S. Kastrup Journal of Medicinal Chemistry 2009 52 (15), 4911-4922 http://dx.doi.org/10.1021/jm900565c
Induced Fit Docking, QM-Polarized Ligand Docking, Prime The Two Enantiomers of Citalopram Bind to the Human Serotonin Transporter in Reversed Orientations Heidi Koldsø, Kasper Severinsen, Thuy Tien Tran, Leyla Celik, Henrik Helligsø Jensen, Ove Wiborg, Birgit Schiøtt, Steffen Sinning Journal of the American Chemical Society 2010 132 (4), 1311-1322 http://dx.doi.org/10.1021/ja906923j
Induced Fit Docking, Glide,Prime Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers, Elizabeth Yuriev Journal of Chemical Information and Modeling, ASAP Article
Glide, Prime MM-GBSA, WaterMap, KNIME Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations Cristiano R. W. Guimaraes, Alan M. Mathiowetz Journal of Chemical Information and Modeling, ASAP Article
Glide, Prime MM-GBSA,Phase Novel Inhibitors of Dengue Virus Methyltransferase: Discovery by in Vitro-Driven Virtual Screening on a Desktop Computer Grid Michael Podvinec, Siew Pheng Lim, Tobias Schmidt, Marco Scarsi, Daying Wen, Louis-Sebastian Sonntag, Paul Sanschagrin, Peter S. Shenkin, Torsten Schwede Journal of Medicinal Chemistry 2010 53 (4), 1483-1495 http://dx.doi.org/10.1021/jm900776m
Glide Improving Binding Specificity of Pharmacological Chaperones That Target Mutant Superoxide Dismutase-1 Linked to Familial Amyotrophic Lateral Sclerosis Using Computational Methods Richard J. Nowak, Gregory D. Cuny, Sungwoon Choi, Peter T. Lansbury, Soumya S. Ray Journal of Medicinal Chemistry 2010 53 (7), 2709-2718 http://dx.doi.org/10.1021/jm901062p
Glide Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening Krishna P. Ravindranathan, Valsan Mandiyan, Anil R. Ekkati, Jae H. Bae, Joseph Schlessinger, William L. Jorgensen Journal of Medicinal Chemistry 2010 53 (4), 1662-1672 http://dx.doi.org/10.1021/jm901386e
Desmond Probing the α-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis Zuojun Guo, Udayan Mohanty, Justin Noehre, Tomi K. Sawyer, Woody Sherman, Goran Krilov Chemical Biology & Drug Design 2010 75 (4), 348-359 http://dx.doi.org/10.1111/j.1747-0285.2010.00951.x
Desmond Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field Devleena Shivakumar, Joshua Williams, Yujie Wu, Wolfgang Damm, John Shelley, Woody Sherman Journal of Chemical Theory and Computation, ASAP Article
LigPrep and QikProp Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers Alexander Chuprina, Oleg Lukin, Robert Demoiseaux, Alexander Buzko, Alexander Shivanyuk Journal of Chemical Information and Modeling, ASAP Article
QSite Importance of the Lactate Dehydrogenase Quaternary Structure in Theoretical Calculations Katarzyna Swiderek, Piotr Paneth The Journal of Physical Chemistry B 2010 114 (9), 3393-3397 http://dx.doi.org/10.1021/jp100026z
MacroModel, Jaguar Triple Recognition of B-DNA by a Neomycin−Hoechst 33258−Pyrene Conjugate Bert Willis, Dev P. Arya Biochemistry 2010 49 (3), 452-469 http://dx.doi.org/10.1021/bi9016796
Applications: Small-molecule modeling
MacroModel Electron Hydration and Ion−Electron Pairs in Water Clusters Containing Trivalent Metal Ions William A. Donald, Maria Demireva, Ryan D. Leib, M. Jeannette Aiken, Evan R. Williams Journal of the American Chemical Society 2010 132 (13), 4633-4640 http://dx.doi.org/10.1021/ja9079385
Jaguar Masked Cyanoacrylates Unveiled by Mechanical Force Matthew J. Kryger, Mitchell T. Ong, Susan A. Odom, Nancy R. Sottos, Scott R. White, Todd J. Martinez, Jeffrey S. Moore Journal of the American Chemical Society 2010 132 (13), 4558-4559 http://dx.doi.org/10.1021/ja1008932
Jaguar Facile Activation of Dihydrogen by a Phosphinito-Bridged Pt(I)−Pt(I) Complex Piero Mastrorilli, Mario Latronico, Vito Gallo, Flavia Polini, Nazzareno Re, Alessandro Marrone, Roberto Gobetto, Silvano Ellena Journal of the American Chemical Society 2010 132 (13), 4752-4765 http://dx.doi.org/10.1021/ja909747r
Jaguar On the Chalcogenophilicity of Mercury: Evidence for a Strong Hg−Se Bond in [TmBut]HgSePh and Its Relevance to the Toxicity of Mercury Jonathan G. Melnick, Kevin Yurkerwich, Gerard Parkin Journal of the American Chemical Society 2010 132 (2), 647-655 http://dx.doi.org/10.1021/ja907523x
Jaguar Dearomatization Reactions of N-Heterocycles Mediated by Group 3 Complexes Kevin L. Miller, Bryan N. Williams, Diego Benitez, Colin T. Carver, Kevin R. Ogilby, Ekaterina Tkatchouk, William A. Goddard III, Paula L. Diaconescu Journal of the American Chemical Society 2010 132 (1), 342-355 http://dx.doi.org/10.1021/ja908489p
Jaguar Phosphinidene Complexes of Scandium: Powerful PAr Group-Transfer Vehicles to Organic and Inorganic Substrates Benjamin F. Wicker, Jennifer Scott, Jose G. Andino, Xinfeng Gao, Hyunsoo Park, Maren Pink, Daniel J. Mindiola Journal of the American Chemical Society 2010 132 (11), 3691-3693 http://dx.doi.org/10.1021/ja100214e
