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

• •  ö  Per Plenge, Lei Shi, Thijs Beuming, Jerez Te, Amy Hauck Newman, Harel Weinstein, Ulrik Gether and Claus J. Loland, "Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter," J. Biol. Chem., 2012, 287, 39316-39326
• •  Fu, J.; Si, P.; Zheng, M.; Chen, L.; Shen, X.; Tang, Y.; Li, W., "Discovery of new non-steroidal FXR ligands via a virtual screening workflow based on Phase shape and induced fit docking," Bioorg. Med. Chem. Lett., 2012, 22(22), 6848-6853
• •  Gemma, S.; Camodeca, C.; Coccone, S.S.; Joshi, B.P.; Bernetti, M.; Moretti, V.; Brogi, S.; de Marcos, M.C.B.; Savini, L.; Taramelli, D.; Basilico, N.; Parapini, S.; Rottmann, M.; Brun, R.; Lamponi, S.; Caccia, S.; Guiso, G.; Summers, R.L.; Martin, R.E.; , "Optimization of 4-aminoquinoline/clotrimazole-Based Hybrid antimalarials: Further structure–activity relationships, in vivo studies, and preliminary toxicity profiling," J. Med. Chem., 2012, 55(15), 6948-6967
• •  ö  Newman, A.H.; Beuming, T.; Banala, A.K.; Donthamsetti, P.; Pongetti, K.; LaBounty, A.; Levy, B.; Cao, J.; Michino, M.; Luedtke, R.P.; Javitch, J.A.; Shi, L., "Molecular determinants of selectivity and efficacy at the dopamine D3 receptor," J. Med. Chem., 2012, 55 (15), 6689–6699
• •  ö  Kalid, O.; Warshaviak, D.T.; Shechter, S.; Sherman, W.; Shacham, S.;, "Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors," J. Comput-Aided Mol. Des., 2012, 26, 1217–1228
• •  Caporuscio, F.; Rastelli, G.; Imbriano, C.; Del Rio, A., "Structure-based design of potent aromatase inhibitors by high-throughput docking," J. Med. Chem., 2011, 54, 4006–4017
• •  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
• •  Du, J.; Sun, H.; Xi, L.; Li, J.; Yang, Y.; Liu, H.; Yao, X., "Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and Prime/MM-GBSA calculation," J. Comp. Chem., 2011, 32(13), 2800-2809
• •  McRobb, F. M.; Capuano, B.; Crosby, I. T.; Chalmers, D. K.; Yuriev, E., "Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors," J. Chem. Inf. Model., 2010, 50, 626–637
• •  Wu, G.; Vashishtha, S.V.; Erve, J.C.L., "Characterization of glutathione conjugates of duloxetine by mass spectrometry and evaluation of in silico approaches to rationalize the site of conjugation for thiophene containing drugs," Chem. Res. Toxicol., 2010, 23, 1393-404
• •  Montalban, A.G.; Boman, E.; Chang, C.D.; Ceide, S.C.; Dahl, R.; Dalesandro, D. et al., "Optimization of alpha-ketoamide based p38 inhibitors through modifications to the region that binds to the allosteric site," Bioorg. Med. Chem. Lett., 2010, 20, 4819-4824
• •  Huang, W.S.; Metcalf, C.A.; Sundaramoorthi, R.; Wang, Y.H.; Zou, D.; Thomas, R.M. et al., "Discovery of  3-[2- (Imidazo[1,2-b]pyridazin-3-yl)ethynyl]-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3- (trifluoromethyl)phenyl] benzamide (AP24534), a Potent, Orally Active Pan-Inhibitor of Breakpoint Cluster Region-Abelson (BCR-ABL) Kinase Including the T315I Gatekeeper Mutant," J. Med. Chem., 2010, 53, 4701-4719
• •  Arhancet, G.B.; Woodard, S.S.; Dietz, J.D.; Garland, D.J.; Wagner, G.M.; Iyanar, K. et al., "Stereochemical Requirements for the Mineralocorticoid Receptor Antagonist Activity of Dihydropyridines," J. Med. Chem., 2010, 53, 4300-4304
• •  Kim, Y.A.; Rawal, R.K.; Yoo, J.; Sharon, A.; Jha, A.K.; Chu, C.K. et al., "Structure-activity relationships of carbocyclic 6-benzylthioinosine analogues as subversive substrates of Toxoplasma gondii adenosine kinase," Bioorg. Med. Chem., 2010, 18, 3403-3412
• •  Craig, I.R.; Essex, J.W.; Spiegel, K., "Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments," J. Chem. Inf. Model., 2010, 50, 511-524
• •  Koldso, H.; Severinsen, K.; Tran, T.T.; Celik, L.; Jensen, H.H.; Wiborg, O. et al., "The Two Enantiomers of Citalopram Bind to the Human Serotonin Transporter in Reversed Orientations," J. Am. Chem. Soc., 2010, 132, 1311-1322
• •  Grilo, L.S.; Carrupt, P.A.; Daina, A., "Stereoselective Block of hERG Channel by Bupivacaine Scrutinized at Molecular Level," Chimia, 2010, 64, 165-169
• •  Azam M.; Powers, J.T.; Einhorn, W.; Huang, W.S.; Shakespeare, W.C.; Zhu, X.T. et al., "AP24163 Inhibits the Gatekeeper Mutant of BCR-ABL and Suppresses In vitro Resistance," Chem. Biol. Drug Des., 2010, 75, 223-227
• •  Liao, C.; Park, J.; Bang, J. K.; Nicklaus, M. C.; Lee, K. S., "Probing Binding Modes of Small Molecule Inhibitors to the Polo-Box Domain of Human Polo-like Kinase 1," ACS Med. Chem. Lett. , 2010, 1, 110–114
• •  Miller, K.J.; Wu, G.Y.; Varnes, J.G.; Levesque, P.; Li, J.L.; Li, D.S. et al., "Position 5.46 of the Serotonin 5-HT2A Receptor Contributes to a Species-Dependent Variation for the 5-HT2C Agonist (R)-9-Ethyl-1,3,4,10b-tetrahydro-7- trifluoromethylpyrazino[2,1-a]isoindol-6(2H)-one: Impact on Selectivity and Toxicological Evaluation," Mol. Pharmacol., 2009, 76, 1211-1219
• •  Cho, Y.; Yao, K.; Pugliese, A.; Malakhova, M. L.; Bode, A. M.; Dong, Z., "A Regulatory Mechanism for RSK2 NH2-Terminal Kinase Activity, (For computational details, please see Supplemental Materials.)," Cancer Res., 2009, 69, 4398-4406
• •  King, A.R.; Dotsey, E.Y.; Lodola, A.; Jung, K.M.; Ghomian, A.; Qiu, Y.; Fu, J.; Mor, M.; Piomelli, D., "Discovery of Potent and Reversible Monoacylglycerol Lipase Inhibitors," Chem. Biol., 2009, 16, 1045-1052
• •  Zhong, H.; Trana, L.M.; Stang, J.L., "Induced-fit docking studies of the active and inactive states of protein tyrosine kinases," J. Mol. Graphics Modell., 2009, 28, 336-346
• •  Shim, J.; Choi, H.S.; Pugliese, A.; Lee, S.; Chae, J.; Choi, B.Y.; Bode, A.M.; Dong, Z., "(-)-Epigallocatechin gallate regulates CD3-mediated T-cell receptor signaling in leukemia through the inhibition of ZAP-70 kinase," J. Biol. Chem., 2008, 283, 28370-28379
• •  Celik, L.; Sinning, S.; Severinsen, K.; Hansen, C.; Møller, M.S.; Bols, M.; Wiborg, O.; Schiøtt, B., "Binding of Serotonin to the Human Serotonin Transporter. Molecular Modeling and Experimental Validation," J. Am. Chem. Soc., 2008, 130, 3853-3865
• •  Salam, N.K.; Huang, T.H.; Kota, B.P.; Kim, M.S.; Li, Y.; Hibbs, D.E., "Novel PPAR-gamma agonists identified from a natural product library: A virtual screening, induced-fit docking and biological assay study," Chem. Biol. Drug Des., 2008, 71, 57-70
• •  Kotsuma, M.; Hanzawa, H.; Iwata, Y.; Takahashi, K.; Tokui, T., "Novel Binding Mode of the Acidic CYP2D6 Substrates Pactimibe and Its Metabolite R-125528," Drug Metab. Dispos., 2008, 36, 1938–1943
• •  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
• •  Gadakar, P.K.; Phukan, S.; Dattatreya, P.; Balaji, V.N., "Pose prediction accuracy in docking studies and enrichment of actives in the active site of GSK-3β ," J. Chem. Inf. Model. , 2007, 47, 1446-1459
• •  Abell, A.D.; Jones, M.A.; Neffe, A.T.; Aitken, S.G.; Cain, T.P.; Payne, R.J.; McNabb, S.B.; Coxon, J.M.; Stuart, B.G.; Pearson, D.; Lee, H.Y.; Morton, J.D., "Investigation into the P3 Binding Domain of m-Calpain Using Photoswitchable Diazo- and Triazene-dipeptide Aldehydes: New Anticataract Agents," J. Med. Chem., 2007, 50, 2916-2920
• •  Harpsøe, K.; Varming, T.; Gouliaev, A.H.; Peters, D.; Liljefors, T., "Identification of a putative binding site for 5-alkyl-benzothiadiazides in the AMPA receptor dimer interface," J. Mol. Graph. Model., 2007, 26, 213-225
• •  Bowman, A.L.; Nikolovska-Coleska, Z.; Zhong, H.; Wang, S.; Carlson, H.A., "Small Molecule Inhibitors of the MDM2-p53 Interaction Discovered by Ensemble-Based Receptor Models," J. Am. Chem. Soc., 2007, 129, 12809 -12814
• •  Maeda, K.; Das, D.; Ogata-Aoki, H.; Nakata, H.; Miyakawa, T.; Tojo, Y.; Norman, R.; Takaoka, Y.; Ding, J.; Arnold, G. F.; Arnold, E.; Mitsuya, H., "Structural and Molecular Interactions of CCR5 Inhibitors with CCR5," J. Biol. Chem., 2006, 281, 2688-12698
• •  ö  Farid, R.; Day, T.; Friesner, R. A.; Pearlstein, R. A., "New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies," Bioorg. & Med. Chem., 2006, 14, 3160-3173
• •  Forouhar, F.; Hussain, M.; Farid, R.; Benach, J.; Abashidze, M.; Edstrom, W. C.; Vorobiev, S. M.; Xiao, R.; Acton, T. B.; Fu, Z.; Kim, J. J.; Miziorko, H. M.; Montelione, G. T.; Hunt, J. F., "Crystal Structures of Two Bacterial HMG-CoA Lyases suggest a common catalytic mechanism among a family of TIM-Barrel Mettalloenyzmes Cleaving Carbon-Carbon Bonds," J. Biol. Chem., 2006, 281, 7533-7545
• •  ö  Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R., "Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects," J. Med. Chem., 2006, 49, 534-553
• •  ö  Sherman, W.; Beard, H. S.; Farid, R., "Use of an Induced Fit Receptor Structure in Virtual Screening," Chemical Biology & Drug Design, 2006, 67, 83-84
• •  Jovanovic, T.; Farid, R.; Friesner, R. A.; McDermott, A. E., "Thermal Equilibrium of High- and Low-Spin Forms of Cytochrome P450-BM3: Repositioning of the Substrate?," J. Am. Chem. Soc., 2005, 127, 13548-13552

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