Some recent publications include:

• Claramunt, R. M.; Herranz, F.; Santa Maria, M. D.; Jaime, C.; de Federico, M.; Elguero, J., "Towards the design of host-guest complexes: biotin and urea derivatives versus artificial receptors", Biosens. Bioelectron., 2004, 20, 1242-1249.
• Litvinchuk, S.; Bollot, G.; Mareda, J.; Som, A.; Ronan, D.; Shah, M. R.; Perrottet, P.; Sakai, N.; Matile, S., "Thermodynamic and kinetic stability of synthetic multifunctional rigid-rod beta-barrel pores: Evidence for supramolecular catalysis", J. Am. Chem. Soc., 2004, 126, 10067-10075.
• Bergstrom, C. A. S.; Wassvik, C. M.; Norinder, U.; Luthman, K.; Artursson, P., "Global and local computational models for aqueous solubility prediction of drug-like molecules", J. Chem. Inf. Comput. Sci., 2004, 44, 1477-1488.
• Kifli, N.; Htar, T. T.; De Clercq, E.; Balzarini, J.; Simons, C., "Novel bicyclic sugar modified nucleosides: synthesis, conformational analysis and antiviral evaluation", Bioorg. Med. Chem., 2004, 12, 3247-3257.
• Cai, M.; Cai, C.; Mayorov, A. V.; Xiong, C.; Cabello, C. M.; Soloshonok, V. A.; Swift, J. R.; Trivedi, D.; Hruby, V. J., "Biological and conformational study of beta-substituted prolines in MT-II template: steric effects leading to human MC5 receptor selectivity", J. Peptide Res., 2004, 63, 116-131.
• Assefa, H.; Kamath, S.; Buolamwini, J. K , "3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors", J. Comput.-Aided Mol. Des., 2004, 17, 475-493.
• Uccello-Barretta, G.; Balzano, F.; Sicoli, G.; Fríglola, C.; Aldana, I.; Monge, A.; Paolino, D.; Guccione, S. , "Combining NMR and molecular modelling in a drug delivery context: investigation of the multi-mode inclusion of a new NPY-5 antagonist bromobenzenesulfonamide into b-cyclodextrin", Bioorg. Med. Chem. 2004, 12, 447-458.
• Hayes, J. M.; Stein, M.; Weiser, J., "Accurate Calculations of Ligand Binding Free Energies: Chiral Separation with Enantioselective Receptors.", J. Phys. Chem. A, 2004, 108, 3572-3580.
• Smith, L.; Zachariah, C.; Thirumoorthy, R.; Rocca, J.; Novak, J.; Hillman, J. D.; Edison, A. S., "Structure and Dynamics of the Lantibiotic Mutacin 1140", Biochemistry, 2003, 42, 10372-10384.
• Simon, C.; Barathieu, K.; Laguerre, M.; Schmitter, J.-M.; Fouquet, E.; Pianet, I.; Dufourc, E. J., "Three-Dimensional Structure and Dynamics of Wine Tannin-Saliva Protein Complexes. A Multitechnique Approach", Biochemistry, 2003, 42, 10385-10395.
• Greenidge, P. A.; Mérette, S. A. M.; Beck, R.; Dodson, G.; Goodwin, C. A.; Scully, M. F.; Spencer, J.; Weiser, J.; Deadman, J. J., "Generation of Ligand Conformations in Continuum Solvent Consistent with Protein Active Site Topology: Application to Thrombin", J. Med. Chem., 2003, 46, 1293-1305.
• Bergstrom, C. A. S.; Norinder, U.; Luthman, K.; Artursson, P., "Molecular Descriptors influencing melting point and their role in classification of solid drugs", J. Chem. Inf. Comput. Sci., 2003, 43, 1177-1185.
• Price, M. L. P.; Guida, W. C.; Jackson, T. C.; Nydick, J. A.; Gladstone, P. L.; Juarez, J. C.; Doñate, F.; Ternansky, R. J., "Design of Novel N-(2,4-Dioxo-1,2,3,4-tetrahydro-thieno[3,2-d]pyrimidin-7-yl)-guanidines as Thymidine Phosphorylase Inhibitors, and Flexible Docking to a Homology Model ", Bioorganic & Medicinal Chem. Lett., 2003, 13, 107-110.
• Taggi, A. E.; Hafez, A. M.; Dudding, T.; Lectka, T., "Molecular mechanics calculations as predictors of enantioselectivity for chiral nucleophile catalyzed reactions", Tetrahedron, 2002, 58, 8351-8356.
• Hoye, T. R.; Ayyad, S.-E. N.; Eklov, B. M.; Hashish, N. E.; Shier, W. T.; El Sayed, K. A.; Hammann, M. T., "Toward Computing Relative Configurations: 16-epi-Latrunculin B, a New Stereoisomer of the Actin Polymerization Inhibitor Latrunculin B", J. Am. Chem. Soc., 2002, 124, 7405-7410.
• Guvench, O.; Weiser, J.; Shenkin, P.S.; Kolossváry, I.; Still, W.C., "Application of the Frozen Atom Approximation to the GB/SA Continuum Model for Solvation Free Energy", J. Comput. Chem., 2002, 23, 214-221.
• Gawley, R. E.; Pinet, S.; Cardona, C. M.; Datta, P. K.; Ren, T.; Guida, W. C.; Nydick, J.; Leblanc, R. M., "Chemosensors for the Marine Toxin Saxitoxin", J. Am. Chem. Soc., 2002, 124, 13448-13453.
• Bostrom, J., "Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools", J. Comput.-Aided Mol. Des., 2001, 15, 1137-1152.
• Reichert, D. E.; Norrby, P. O.; Welch, M. J., "Molecular modeling of bifunctional chelate peptide conjugates. 1. Copper and indium parameters for the AMBER force field", Inorg. Chem., 2001, 40, 5223-5230.
• Keseru, G. M.; Kolossvary, I., "Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase", J. Am. Chem. Soc., 2001, 123, 12708-12709.
• Kolossvary, I.; Keseru, G. M., "Hessian-Free Low-Mode Conformational Search for Large-Scale Protein Loop Optimization: Application to c-jun N-Terminal Kinase JNK3," J. Comp. Chem., 2001, 22(1), 21-30.
• Thirumoorthy, R.; Holder, J. R.; Bauzo, R. M.; Richards, N. G. J.; Edison, A. S.; Haskell-Luevano, C., "Novel Agouti-Related-Protein-Based Melanocortin-1 Receptor Antagonist", J. Med. Chem., 2001, 44, 4114-4124.
• Greenidge, P.A; Weiser, J., "A Comparison of Methods for Pharmacophore Generation with the Catalyst Software and their Use for 3D-QSAR: Application to a Set of 4-aminopyridine Thrombin Inhibitors", Mini Rev. Med. Chem., 2001, 1, 79-87.
• Christianson, L. A.; Lucero, M. J.; Appella, D. H.; Klein, D. A.; Gellman, S. H., "Improved treatment of cyclic beta-amino acids and successful prediction of beta-Peptide secondary structure using a modified force field: AMBER*C", J. Comput. Chem., 2000, 21, 763-773.
• Korner, S. K.; Tucci, F. C.; Rudkevich, D. M.; Heinz, T.; Rebek, J., "A self-assembled cylindrical capsule: New supramolecular phenomena through encapsulation", Chem. – Eur. J., 2000, 6, 187-195.
  
• Etzkorn, F.A. ; Travins, J.M., " Stereoselective deuterium labeling of proR b-protons in the NMR structure determination of a helix-turn-helix turn peptidomimetic. ", J. Peptide Res., 2000, 55, 436-446.
• Modica, M.; Santagati, M.; Guccione, S.; Russo, F.; Cagnotto, A.; Goegan, M.; Mennini, T., "Design, synthesis and binding properties of novel and selective 5-HT3 and 5-HT4 receptor ligands", Eur. J. Med. Chem. 2000, 35 (12), 1065. Erratum: ibid 2001, 36 287-301.
• Smith, A. B., III; Wang, W.; Sprengeler, P. A.; Hirschmann, R., "Design, Synthesis, and Solution Structure of a Pyrrolinone-Based Β-Turn Peptidomimetic" J. Am. Chem. Soc. 2000, 122, 11037-11038.
• Snyder, J. P.; Nevins, N.; Cicero, D. O.; Jansen, J., "The Conformations of Taxol in Chloroform", J. Am. Chem. Soc. 2000, 122, 724-725.
• Strittmatter, E. F.; Williams, E. R., "Structures of Protonated Arginine Dimer and Bradykinin Investigated by Density Functional Theory: Further Support for Stable Gas-Phase Salt Bridges", J. Phys. Chem. A. 2000, 104, 6069-6076.