Glide

A complete solution for ligand-receptor docking

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

  • •  Palakurti, R.; Sriram, D.; Yogeeswari, P.; Vadrevu, R., "Multiple e-Pharmacophore Modeling Combined with High-Throughput Virtual Screening and Docking to Identify Potential Inhibitors of β-Secretase(BACE1)," Mol. Inf., 2013, 32, 385-398
  • •  ö  Osguthorpe, D.J.; Sherman, W.; Hagler, A.T., "Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering," Chem. Biol. Drug Des.,, 2012, 80(2), 182-193
  • •  ö  Osguthorpe D.J.; Sherman, W.; Hagler, A.T., "Exploring protein flexibility: Incorporating structural ensembles from crystal structures and simulation into virtual screening protocols," J. Phys. Chem. B, 2012, 116(23), 6952-6959
  • •  ö  Repasky, M.P.; Murphy, R.B.; Banks, J.L.; Greenwood, J.R.; Tubert-Brohman, I.; Bhat, S.; Friesner, R.A., "Docking performance of the Glide program as evaluated on the Astex and DUD datasets: A complete set of Glide SP results and selected results for a new scoring function integrating WaterMap and Glide," J. Comput-Aided Mol. Des., 2012, 26, 787-799
  • •  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
  • •  Wu, D.; Wang, Q.; Assary, R.S.; Broadbelt, L.J.; Krilov, G., "A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate," J. Chem. Inf. Model, 2011, 51, 1634-47
  • •  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
  • •  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
  • •  Albers, H.M.H.G.; Hendrickx, L.J.D.; van Tol, R.J.P.; Hausmann, J; Perrakis, A.; Ovaa, H., "Structure-based design of novel boronic acid-based inhibitors of autotaxin," J. Med. Chem., 2011, 54, 4619-26
  • •  Cortial, S.; Chaignon, P.; Iorga, B.I.; Aymerich, S.; Truan G.; Gueguen-Chaignon, V. et al., "NADH Oxidase Activity of Bacillus subtilis Nitroreductase NfrA1: Insight into its Biological Role," FEBS Lett., 2010, 584, 3916-22
  • •  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, 626-37
  • •  Shen, J.; Tan, C.; Zhang, Y.; Li, X.; Li, W.; Huang, J.; Shen, X.; Tang, Y., "Discovery of Potent Ligands for Estrogen Receptor β by Structure-Based Virtual Screening," J. Med. Chem., 2010, 53, 5361-5365
  • •  Ali, S. T.; Jahangir, S.; Karamat, S.; Fabian, W. M. F.; Nawara, K.; Kóňa, J., "Theoretical Study on the Redox Cycle of Bovine Glutathione Peroxidase GPx1: pKa Calculations, Docking, and Molecular Dynamics Simulations," J. Chem. Theory Comput., 2010, 6, 1670–1681
  • •  Podvinec, M.; Lim, S. P.; Schmidt, T.; Scarsi, M.; Wen, D.; Sonntag, L.; Sanschagrin, P.; Shenkin, P. S.; Schwede, T., "Novel Inhibitors of Dengue Virus Methyltransferase: Discovery by in Vitro-Driven Virtual Screening on a Desktop Computer Grid," J. Med. Chem., 2010, 53, 1483–1495
  • •  ö  Loving, K.; Alberts, I.; Sherman, W., "Computational Approaches for Fragment-Based and De Novo Design," Curr. Top. Med. Chem., 2010, 10, 14-32
  • •  Ravindranathan, K. P.; Mandiyan, V.; Ekkati, A. R.; Bae, J. H.; Schlessinger, J.; Jorgensen, W. L., "Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening," J. Med. Chem., 2010, 53, 1662–1672
  • •  Agostino, M.; Jene, C.; Byle, T.; Ramsland, P. A.; Yuriev, E., "Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures," J. Chem. Inf. Model., 2009, 49, 2749-2760
  • •  Benltifa, M.; Hayes, J. M.; Vidal, S.; Gueyrard, D.; Goekjian, P. G.; Praly, J.; Kizilis, G.; Tiraidis, C.; Alexacou, K.; Chrysina, E. D.; Zographos, S. E.; Leonidas, D. D.; Archontis, G.; Oikonomakos, N. G., "Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitors," Bioorg. Med. Chem., 2009, 17, 7368-7380
  • •  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
  • •  Kawatkar, S.; Wang, H.; Czerminski, R.; Joseph-McCarthy, D., "Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide," J. Comput. Aided Mol. Des., 2009, 23, 527-539
  • •  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
  • •  ö  Rao, S.; Sanschagrin, P. C.; Greenwood, J. R.; Repasky, M. P.; Sherman, W.; Farid, R., "Improving database enrichment through ensemble docking," J. Comput. Aided. Mol. Des., 2008, 22, 621-627
  • •  Pierce, A.C.; Jacobs, M.; and Stuver-Moody, C., "Docking Study Yields Four Novel Inhibitors of the Protooncogene Pim-1 Kinase," J. Med. Chem., 2008, 51, 1972–1975
  • •  Pauly, G.T.; Loktionova, N.A.; Fang, Q.; Vankayala, S.L.; Guida, W.C.; Pegg, A.E., "Substitution of Aminomethyl at the Meta-Position Enhances the Inactivation of O(6)-Alkylguanine-DNA Alkyltransferase by O(6)-Benzylguanine," J. Med. Chem., 2008, 51, 7144–7153
  • •  Bembenek, S.D.; Keith, J.M.; Letavic, M.A.; Apodaca, R.; Barbier, A.J.; Dvorak, L.; Aluisio, L.; Miller, K.L.; Lovenberg, T.W.; Carruthers, N.I., "Lead identification of acetylcholinesterase inhibitors–histamine H3 receptor antagonists from molecular modeling," Bioorg. & Med. Chem., 2008, 16, 2968-2973
  • •  Lawrence, S.H.; Ramirez, U.D.; Tang, L.; Fazliyez, F.; Kundrat, L.; Markham, G.D.; Jaffe, E.K., "Shape shifting leads to small-molecule allosteric drug discovery," Chem Biol., 2008, 15, 586-96
  • •  Cheng, J.-F.; Zapf, J.; Takedomi, K.; Fukushima, C.; Ogiku, T. Zhang S.-H.; Yang, G.; Sakurai, N.; Barbosa, M.; Jack, R.; Xu, K., "Combination of Virtual Screening and High Throughput Gene Profiling for Identification of Novel Liver X Receptor Modulators," J. Med. Chem., 2008, 51, 2057-2061
  • •  Degel, B.; Staib, P.; Rohrer, S.; Scheiber, J.; Martina, E.; Büchold, C.; Baumann, K.; Morschhäuser, J.; Schirmeister, T., "Cis-Configured Aziridines Are New Pseudo-Irreversible Dual-Mode Inhibitors of Candida albicans Secreted Aspartic Protease 2," Chem. Med. Chem., 2008, 3, 302-315
  • •  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
  • •  Siddiquee, K.; Zhang, S.; Guida, W.C.; Blaskovich, M.A.; Greedy, B.; Lawrence, H.R.; Yip, M.L.; Jove, R.; McLaughlin, M.M.; Lawrence, N.J.; Sebti, S.M.; Turkson J., "Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity," Proc. Natl. Acad. Sci., 2007, 104, 7391–7396
  • •  Zhou, Z.; Felts, A. K.; Friesner, R. A.; Levy, R. M., "Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets," J. Chem. Inf. Model, 2007, 47, 1599–1608
  • •  Englebienne, P.; Fiaux, H.; Kuntz, D. A.; Corbeil, C. R.; Gerber-Lemaire, S.; Rose, D. R.; Moitessier, N., "Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: A comparison with crystallography," Proteins: Structure, Function, and Bioinformatics, 2007, 69, 160–176
  • •  Tripathy, R.; Ghose, A.; Singh, J.; Bacon, E. R.; Angeles, T. S.; Yang, S. X.; Albom, M. S.; Aimone, L. S.; Herman, J. L.; Mallamo, J. P., "1,2,3-Thiadiazole substituted pyrazolones as potent KDR/VEGFR-2 kinase inhibitors," Bioorg. Med. Chem. Lett., 2007, 17, 1793–1798
  • •  Lyne, P. D.; Lamb, M. L.; Saeh, J. C., "Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring," J. Med. Chem., 2006, 49, 4805-4808
  • •  Pomel, V.; Klicic, J.; Covini, D.; Church, D.D.; Shaw, J.P.; Roulin, K.; Burgat-Charvillon, F.; Valognes, D.; Camps, M.; Chabert, C.; Gillieron, C.; Françon, B.; Perrin, D.; Leroy, D.; Gretener, D.; Nichols, A.; Vitte, P.A.; Carboni, S.; Rommel, C.; Schwa, "Furan-2-ylmethylene thiazolidinediones as novel, potent, and selective inhibitors of phosphoinositide 3-kinase gamma," J. Med. Chem., 2006, 3857-3871
  • •  ö  Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren,T. A.; Sanschagrin, P. C.; Mainz, D. T., "Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes," J. Med. Chem., 2006, 49, 6177–6196
  • •  Kim, K. W.; Wang, Z.; Busby, J.; Tsuruda, T.; Chen, M.; Hale, C.; Castro, V. M.; Svensson, S.; Nybo, R.; Xiong, F.; Wang, M., "The role of tyrosine 177 in human 11β-hydroxysteroid dehydrogenase type 1 in substrate and inhibitor binding: an unlikely hydrogen bond donor for the substrate," Biochem. Biophys. Acta, Proteins Proteomics, 2006, 1764, 824–830
  • •  ö  Cho, A. E.; Guallar, V.; Berne, B.; Friesner, R. A., "Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach," J. Comput. Chem., 2005, 26, 915–931
  • •  Krovat, E. M.; Steindl, T.; Langer, T., "Recent Advances in Docking and Scoring," Current Computer-Aided Drug Design, 2005, 1, 93–102
  • •  Kontoyianni, M.; Sokol, G. S.; McClellan, L.M., "Evaluation of library ranking efficacy in virtual screening," J. Comput. Chem., 2005, 26, 11–22
  • •  Kirkpatrick, P., "Virtual screening: Gliding to success," Nature Reviews Drug Discovery, 2004, 3, 299
  • •  ö  Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L., "Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening," J. Med. Chem., 2004, 47, 1750–1759
  • •  ö  Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.; Shenkin, P. S., "Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy," J. Med. Chem., 2004, 47, 1739–1749
  • •  Klon, A. E.; Glick, M.; Davies, J. W., "Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease," J. Chem. Inf. Comput. Sci., 2004, 44, 2216–2224
  • •  Ruddat, V. C.; Mogul, R.; Chorny, I.; Chen, C.; Perrin, N.; Whitman, S.; Kenyon, V.; Jacobson, M. P.; Bernasconi, C. F.; Holman, T. R., "Tryptophan 500 and Arginine 707 Define Product and Substrate Active Site Binding in Soybean Lipoxygenase-1," Biochemistry, 2004, 43, 13063–13071
  • •  Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D., "Comparative evaluation of eight docking tools for docking and virtual screening accuracy," Proteins, 2004, 57, 225–242
  • •  Perola, E.; Walters, W.P.; Charifson, P.S., "A Detailed Comparison of Current Docking and Scoring Methods on Systems of Pharmaceutical Relevance," Proteins, 2004, 56, 235–249
  • •  Klon, A. E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J. W., "Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results," J. Med. Chem., 2004, 47, 2743–2749
  • •  Bytheway, I.; Cochran, S., "Validation of Molecular Docking Calculations Involving FGF-1 and FGF-2," J. Med. Chem., 2004, 47, 1683-1693
  • •  Kontoyianni, M.; McClellan, L. M.; Sokol, G. S., "Evaluation of Docking Performance: Comparative Data on Docking Algorithms," J. Med. Chem., 2004, 47, 558–565
  • •  Schulz-Gasch, T; Stahl, M., "Binding site characteristics in structure-based virtual screening: evaluation of current docking tools," J. Mol. Mod., 2003, 9, 47–57
  • •  Wu, T. Y. H.; Wagner, K. W.; Bursulaya, B.; Schultz, P. G.; Deveraux, Q. L., "Development and Characterization of Nonpeptidic Small Molecule Inhibitors of the XIAP/Caspase-3 Interaction," Chemistry & Biology, 2003, 10, 759–767
  • •  Kuo, G.-H.; Prouty, C.; DeAngelis, A.; Shen, L.; O'Neill, D. J.; Shah, C.; Connolly, P. J.; Murray, W. V.; Conway, B. R.; Cheung, P.; Westover, L.; Xu, J. Z.; Look, R. A.; Demarest, K. T.; Emanuel, S.; Middleton, S. A.; Jolliffe, L.; Beavers, M. P.; Chen,, "Synthesis and Discovery of Macrocyclic Polyoxygenated Bis-7-azaindolylmaleimides as a Novel Series of Potent and Highly Selective Glycogen Synthase Kinase-3 Inhibitors," J. Med. Chem., 2003, 46, 4021–4031
  • •  Nilsson, J. W.; Kvarnstrom, I.; Musil, D.; Nilsson, I.; Samulesson, B., "Synthesis and SAR of Thrombin Inhibitors Incorporating a Novel 4-Amino-Morpholinone Scaffold: Analysis of X-ray Crystal Structure of Enzyme Inhibitor Complex," J. Med. Chem., 2003, 46, 3985–4001
  • •  Bjerrum, E. J.; Kristensen, A. S.; Pickering, D. S.; Greenwood, J. R.; Nielsen, B.; Liljefors, T.; Schousboe, A.; Brauner-Osborne, H.; Madsen, U., "Design, Synthesis, and Pharmacology of a Highly Subtype-Selective GluR1/2 Agonist, (RS)-2-Amino-3-(4-chloro-3-hydroxy-5-isoxazolyl)propionic Acid (Cl-HIBO)," J. Med. Chem., 2003, 46, 2246–2249
  • •  Brehm, L.; Greenwood, J. R.; Hansen, K. B.; Nielsen, B.; Egebjerg, J.; Stensbol, T. B.; Brauner-Osborne, H.; Slok, F. A.; Kronborg, T. T. A.; Krogsgaard-Larsen, P., "(S)-2-Amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl) propionic Acid, a Potent and Selective Agonist at the GluR5 Subtype of Ionotropic Glutamate Receptors. Synthesis, Modeling, and Molecular Pharmacology," J. Med. Chem., 2003, 46, 1350–1358
  • •  Thorstensson, F.; Kvarnstrom, I.; Musil, D.; Nilsson, I.; Samuelsson, B., "Synthesis of Novel Thrombin Inhibitors. Use of Ring-Closing Metathesis Reactions for Synthesis of P2 Cyclopentene- and Cyclohexenedicarboxylic Acid Derivatives," J. Med. Chem., 2003, 46, 1165–1179
  • •  Bunch, L.; Liljefors, T.; Greenwood, J. R.; Frydenvang, K.; Brauner-Osborne, H.; Krogsgaard-Larsen, P.; Madsen, U., "Rational Design, Synthesis, and Pharmacological Evaluation of 2-Azanorbornane-3-exo,5-endo-dicarboxylic Acid: A Novel Conformationally Restricted Glutamic Acid Analogue," J. Org. Chem., 2003, 68, 1489–1495
  • •  Johansen, T. N.; Greenwood, J. R.; Frydenvang, K.; Madsen, U.; Krogsgaard-Larsen, P., "Stereostructure-Activity Studies on Agonists at the AMPA and Kainate Subtypes of Ionotropic Glutamate Receptors," Chirality, 2003, 15, 167–179
  • •  Neamati, N.; Lin, Z.; Karki, R. G.; Orr, A.; Cowansage, K.; Strumberg, D.; Pais, G. C. G.; Voigt, J. H.; Nicklaus, M. C.; Winslow, H. E.; Zhao, H.; Turpin, J. A.; Yi, J.; Skalka, A. M.; Burke, T. R., Jr.; Pommier, Y., "Metal-Dependent Inhibition of HIV-1 Integrase," J. Med. Chem., 2002, 45, 5661–5670
  • •  lausen, R. P.; Brauner-Osborne, H.; Greenwood, J. R.; Hermit, M. B.; Stensbol, T. B.; Nielsen, B.; Krogsgaard-Larsen, P., "Selective Agonists at Group II Metabotropic Glutamate Receptors: Synthesis, Stereochemistry, and Molecular Pharmacology of (S)- and (R)-2-Amino-4-(4-hydroxy[1,2,5]thiadiazol-3-yl) butyric Acid," J. Med. Chem., 2002, 45, 4240–4245
  • •  Zhang, L., E. Gallicchio, R. Friesner, and R.M. Levy, "Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations," J. Comp. Chem., 2001, 22, 591–607
  • ö indicates papers (co)authored by Schrödinger scientist(s).
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