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
http://dx.doi.org/10.1021/ci900444q
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
http://dx.doi.org/10.1021/ci900497d
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
http://dx.doi.org/10.1021/ct900587b
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
http://dx.doi.org/10.1021/ci900464s
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