Below are selected publications from all recent years; please check here to cite the use of MacroModel

• •  ö  Lupyan, D.; Abramov, Y.A.; Sherman, W., "Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation," J. Comput. Aided Mol. Des., 2012, 26, 1195-1205
• •  William, A.D.; Lee, A.C.-H.; Blanchard, S.; Poulsen, A.; Teo, E.L.; Nagaraj, H. et al., "Discovery of the macrocycle 11-(2-Pyrrolidin-1-yl-ethoxy)-14,19-dioxa-5,7,26-triaza-tetracyclo[19.3.1.1(2,6).1(8,12)]heptacosa-1(25),2(26),3,5,8,10,12(27),16,21,23-decaene (SB1518), a potent Janus kinase 2/fms-Like tyrosine kinase-3 (JAK2/FLT3) Inhibitor for the treatment of myelofibrosis and lymphoma," J. Med. Chem., 2011, 54, 4638-4658
• •  Yoo, J.; Medina-Franco, J.L., "Trimethylaurintricarboxylic Acid Inhibits Human DNA Methyltransferase 1: Insights From Enzymatic and Molecular Modeling Studies," J. Mol. Model., Article ASAP, 2011, 18(4), 1583-1589
• •  Ghosh, K.; Sen, T., "(rac)-1,1'-binaphthyl-based simple receptors designed for fluorometric discrimination of maleic and fumaric acids," J. Phys. Chem. B, 2011, 115, 8597-608
• •  Gil, S.; Palomino-Schätzlein, M.; Burusco, K. K.; Jaime, C.; Virgili, A., "Molecular tweezers for enantiodiscrimination in NMR: Di-(R,R)-1-[10-(1-hydroxy-2,2,2-trifluoroethyl)-9-anthryl]-2,2,2-trifluoroethyl benzenedicarboxylates," Chirality, 2010, 22, 548–556
• •  Salameh, B.A.; Cumpstey, I.; Sundin, A.; Leffler, H.; Nilsson, U.J., "1H-1,2,3-Triazol-1-yl thiodigalactoside derivatives as high affinity galectin-3 inhibitors," Bioorg. Med. Chem. Lett., 2010, 18, 5367-5378
• •  Luedtke, G.R.; Schinzel, K.; Tan, X.; Tester, R.W.; Nashashibi, I.; Xu, Y. et al., "Amide-based inhibitors of p38α MAP kinase. Part 1: Discovery of novel N-pyridyl amide lead molecules," Bioorg. Med. Chem. Lett., 2010, 20, 2556-2559
• •  Andersen, N.H.; Lassen, P.R.; Freedman, T.B.; Nafie, L.A.; Strømgaard, K.; Hemmingsen, L., "Structure and absolute configuration of ginkgolide B characterized by IR- and VCD spectroscopy," Chirality, 2010, 22, 217-223
• •  Rajendar, B.; Rajendran, A.; Sato, Y.; Nishizawa, S.; Teramae, N., "Effect of methyl substitution in a ligand on the selectivity and binding affinity for a nucleobase: A case study with isoxanthopterin and its derivatives," Bioorg. Med. Chem., 2009, 17, 351-359
• •  Alexi, X.; Kasiotis, K.M.; Fokialakis, N.; Lambrinidis, G.; Meligova, A.; Mikros, E. et al., "Differential estrogen receptor subtype modulators: Assessment of estrogen receptor subtype-binding selectivity and transcription-regulating properties of new cycloalkyl pyrazoles," J. Steroid Biochem. Mol. Biol., 2009, 117, 159-167
• •  Guimarães, C. R. W.; Cardozo, M., "MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization," J. Chem. Inf. Model., 2008, 48, 958–970
• •  Uccello-Barretta, G.; Balzano, F.; Bardoni, S.; Vanni, L.; Giuratob, L.; Guccione, S., "Chiral discrimination processes by C9 carbamate derivatives of dihydroquinine: interaction mechanisms of diastereoisomeric 9-O-[(S)- or (R)-1-(1-naphthyl)ethylcarbamate]dihydroquinine and the two enantiomers of N-(3,5-dinitrobenzoyl)alanine methyl ester ," Tetrahedron: Asymmetry , 2008, 19, 1084–1093
• •  Ballet, S.; Mayorov, A.V.; Cai, M.; Tymecka, D.; Chandler, K.B.; Palmer, E.S.; Rompaey, K.V.; Misicka, A.; Tourwé, D.; Hruby, V.J., "Novel selective human melanocortin-3 receptor ligands: use of the 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one (Aba) scaffold," Bioorg. Med. Chem. Lett., 2007, 17, 2492-2498
• •  Buey, R.M.; Calvo, E.; Barasoain, I.; Pineda, O.; Edler, M.C.; Matesanz, R. et al., "Cyclostreptin binds covalently to microtubule pores and lumenal taxoid binding sites," Nat. Chem. Biol., 2007, 3, 117-125
• •  Engel, S.; Gershengorn, M. C., "Thyrotropin-releasing hormone and its receptors--a hypothesis for binding and receptor activation," Pharmacol. Ther., 2007, 113, 410-419
• •  Ferrand, Y.; Crump, M.P.; Davis, A.P., "A synthetic lectin analog for biomimetic disaccharide recognition," Science, 2007, 318, 619-622
• •  Leach, K.L.; Swaney, S.M.; Colca, J.R.; McDonald, W.G.; Blinn, J.R.; Thomasco, L.M.; Gadwood, R.C.; Shinabarger, D.; Xiong, L.; Mankin, A.S., "The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria," Mol. Cell., 2007, 26, 393-402
• •  Kim, Y.A.; Sharon, A.; Chu, C.K.; Rais, R.H.; Al Safarjalani, O.N.; Naguib, F.N.M.; el Kouni, M.H., "Synthesis, biological evaluation and molecular modeling studies of N-6-benzyladenosine analogues as potential anti-toxoplasma agents," Biochem. Pharmacol., 2007, 73, 1558-1572
• •  Sum, C. S.; Tikhonova, I. G.; Neumann, S.; Engel, S.; Raaka, B. M.; Costanzi, S.; Gershengorn, M.C., "Identification of Residues Important for Agonist Recognition and Activation in GPR40," J. Biol. Chem. , 2007, 282, 29248-29255
• •  Toba, T.; Murata, K.; Nakanishi, K.; Takahashi, B.; Takemoto, N.; Akabane, M.; Nakatsuka, T.; Imajo, S.; Yamamura, T.; Miyake, S; Annoura, H., "Minimum structure requirement of immunomodulatory glycolipids for predominant Th2 cytokine induction and the discovery of non-linear phytosphingosine analogs," Bioorg. Med. Chem. Lett., 2007, 17, 2781-2784
• •  Ragusa, A.; Hayes, J. M.; Light, M. E.; Kilburn, J. D., "Predicting Enantioselectivity: Computation as an Efficient "Experimental" Tool for Probing Enantioselectivity," Eur. J. Org. Chem., 2006, 16, 3545-3549
• •  Ercanli, T.; Boyd, D.B., "Exploration of the conformational space of a polymeric material that inhibits human immunodeficiency virus," J. Chem. Inf. Model., 2006, 46, 1321-1333
• •  Guida, W.C.; Hamilton, A.D.; Crotty, J.W.; Sebti, S.M., "Protein farnesyltransferase: Flexible docking studies on inhibitors using computational modeling," J. Comput. Aided Mol. Des., 2005, 19, 871-85
• •  Cochran, S.; Li, C.P.; Bytheway, I., "An Experimental and Molecular-Modeling Study of the Binding of Linked Sulfated Tetracyclitols to FGF-1 and FGF-2," ChemBioChem, 2005, 6, 1882-1890
• •  Tafi, A.; Agamennone, M.; Tortorella, P.; Alcaro, S.; Gallina, C.; Botta, M., "AMBER force field implementation of the boronate function to simulate the inhibition of beta-lactamases by alkyl and aryl boronic acids," Eur. J. Med. Chem., 2005, 40, 1134-1142
• •  Ercanli, T.; Boyd, D.B., "Evaluation of computational chemistry methods: crystallographic and cheminformatics analysis of aminothiazole methoximes," J. Chem. Inf. Model., 2005, 45, 591-601
• •  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 β-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 Thromb," 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, 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
• •  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 proRβ-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, 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

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