Selected publications, all recent years:

Brogi, S.; Corelli, F.; Di Marzo, V.; Ligresti, A.; Mugnaini, C.; Pasquini, S.; Tafi, A., "Three-dimensional quantitative structure-selectivity relationships analysis guided rational design of a highly selective ligan for the cannabiniod receptor 2," Eur. J. Med. Chem., 2011, 46, 547-555

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

Durdagi, S.; Duff, H.J.; Noskov, S.Y., “Combined receptor and ligand-based approach to the universal pharmacophore model development for studies of drug blockade to the hERG1 pore domain,” J. Chem. Inf. Model., 2011, 51, 463-74.

Yoo, J.; Medina-Franco, J. L., "Trimethylaurintricarboxylic Acid Inhibits Human DNA Methyltransferase 1: Insights From Enzymatic and Molecular Modeling Studies," J. Mol. Model., 2011, Article ASAP

Yoo, J.; Medina-Franco, J.L., "Homology Modeling, Docking and Structure-Based Pharmacophore of Inhibitors of DNA Methyltransferase," J. Comput. Aided Mol. Des., 2011, 25, 555-567

Tawari, N. R.; Degani, M. S., "Pharmacophore Mapping and Electronic Feature Analysis for a Series of Nitroaromatic Compounds with Antitubercular Activity," J. Comput. Chem., 2010, 31, 739–751.

Bag, S.; Tawari, N. R.; Degani, M. S., "Insight into Inhibitory Activity of Mycobacterial Dihydrofolate Reductase Inhibitors by In-silico Molecular Modeling Approaches," QSAR Comb. Sci., 2009, 28, 296-311.

ö  Salam, N. K.; Nuti, R.; Sherman, W., "Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis," J. Chem. Inf. Model., 2009, 49, 2356–2368.

Hall, M. D.; Salam, N. K.; Hellawell, J. L.; Fales, H. M.; Kensler, C. B.; Ludwig, J. A.; Szakács, G.; Hibbs, D. E.; Gottesman, M. M., "Synthesis, Activity, and Pharmacophore Development for Isatin-β-thiosemicarbazones with Selective Activity toward Multidrug-Resistant Cells," J. Med. Chem., 2009, 52, 3191–3204.

ö  Loving, K.; Salam, N. K.; Sherman, W., "Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation," J. Comput. Aided Mol. Des., 2009, 23, 541–554

Tawari, N. R.; Bag, S.; Degani, M. S., "Pharmacophore mapping of a series of pyrrolopyrimidines, indolopyrimidines and their congeners as multidrug resistance-associated protein (MRP1) modulators," J. Mol. Model., 2008, 14, 911–921.

Kumar, R. J.; Chebib, M.; Hibbs, D. E.; Kim, H.; Johnston, G. A. R.; Salam, N. K.; Hanrahan, J. R., "Novel γ-Aminobutyric Acid ρ1 Receptor Antagonists; Synthesis, Pharmacological Activity and Structure−Activity Relationships," J. Med. Chem., 2008, 51, 3825-3840.

Shamovsky, I.; Connolly, S.; David, L.; Ivanova, S.; Nordé, B.; Springthorpe, B.; Urbahns, K., "Overcoming Undesirable hERG Potency of Chemokine Receptor Antagonists Using Baseline Lipophilicity Relationships," J. Med. Chem., 2008, 51, 1162-1178.

Lather, V.; Kristam, R.; Saini, J.; Karthikeyan, N.; Balaji, V., "QSAR models for prediction of glycogen synthase kinase-3β inhibitory activity of indirubin derivatives," QSAR and Combinatorial Science, 2008, 27, 718-728.

Telvekar, V.; Kundaikar, H.; Patel, K.; Chaudhari, H., "3-D QSAR and molecular docking studies on aryl benzofuran-2-yl ketoxime derivatives as candida albicans N-myristoyl transferase inhibitors," QSAR and Combinatorial Science, 2008, 27, 1193-1203.

Anghelescu, A. V.; DeLisle, R. K.; Lowrie, J. F.; Klon, A. E.; Xie, X.; Diller, D. J., "Technique for Generating Three-Dimensional Alignments of Multiple Ligands from One-Dimensional Alignments," J. Chem. Inf. Model., 2008, 48, 1041-1054.

Gerlach, C.; Broughton, H.; Zaliani, A., "FTree query construction for virtual screening: a statistical analysis," J. Comput. Aided Mol. Des., 2008, 22, 111-118.

Jacobsson, M.; Garedal, M.; Schultz, J.; Karle?n, A., "Identification of Plasmodium falciparum Spermidine Synthase Active Site Binders through Structure-Based Virtual Screening," J. Med. Chem., 2008, 51, 2777–2786.

Narkhede, S. S.; Degani, M. S., "Pharmacophore Refinement and 3D-QSAR Studies of Histamine H3 Antagonists," QSAR Comb. Sci., 2007, 26, 744–753.

Evans, D.A.; Doman, T.N.; Thorner, D.A.; Bodkin, M.J., "3D QSAR Methods: Phase and Catalyst Compared," J. Chem. Inf. Model, 2007, 47, 1248-1257.

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.