BioSolveIT GmbH - literature corner

literature corner

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In this section we collect all articles that have been reviewed in our newsletter literature corner.

	*Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping.* Alessandro Pedretti, Laura De Luca, Cristina Sciarrillo, and Giulio Vistoli ChemMedChem 3(1):79-90. (2008)
	*Selection of a Respiratory Syncytial Virus Fusion Inhibitor Clinical Candidate. 2. Discovery of a Morpholinopropylaminobenzimidazole Derivative (TMC353121)* Jean-François Bonfanti, Christophe Meyer, Frédéric Doublet, Jérôme Fortin, Philippe Muller, Laurence Queguiner, Tom Gevers, Peggy Janssens, Heidi Szel, Rudy Willebrords, Philip Timmerman, Koen Wuyts, Pieter van Remoortere, Frans Janssens, Piet Wigerinck, and Koen Andries J. Med. Chem. 51(4):875-96. (2008)
	*Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.* Zaheer-ul-Haq, Reaz Uddin, Hongbin Yuan, Pavel A. Petukhov, M. Iqbal Choudhary, and Jeffry D. Madura J. Chem. Inf. Model. 48(5):1092-103. (2008)
	*A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists.* Stanislav Engel, Amanda P. Skoumbourdis, John Childress, Susanne Neumann, Jeffrey R. Deschamps, Craig J. Thomas, Anny-Odile Colson, Stefano Costanzi, and Marvin C. Gershengorn J. Am. Chem. Soc. 130(15):5115-23. (2008)

	*Identification of novel inhibitors of bacterial surface enzyme Staphylococcus aureus Sortase A* Bala C. Chenna, Bidhan A. Shinkre, Jason R. King, Aaron L. Lucius, Sthanam V. L. Narayana and Sadanandan E. Velu Bioorg. Med. Chem. Lett., 18, 380385, (2008)
	*Use of 3D QSAR Models for Database Screening: A Feasibility Study* Alexander Hillebrecht and Gerhard Klebe J. Chem. Inf. Model., 48 (2), 384-96, (2008)
	*Human Microsomal Prostaglandin E Synthase-1 (mPGES-1) Binding with Inhibitors and the Quantitative Structure-Activity Correlation* Mohamed D. M. AbdulHameed, Adel Hamza, Junjun Liu, Xiaoqin Huang and Chang-Guo Zhan J. Chem. Inf. Model., 48 (1), 179-85, (2008)
	*SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering* Robert Fischer and Matthias Rarey J. Chem. Inf. Model., 48 (4), 1341-53, (2007)

	*Discovery and optimization of novel, non-steroidal glucocorticoid receptor modulators* Nicholas C. Ray, Robin D. Clark, David E. Clark, Karen Williams, H.G. Hickin, Peter H. Crackett, Hazel J. Dyke, Peter M. Lockey, Melanie Wong, René Devos, Anne White, and Joseph K. Belanoff. Bioorg. Med. Chem. Lett., 17, (17), 4901-4905, (2007)
	*GPCR Structure-Based Virtual Screening Approach for CB2 Antagonist Search* Jian-Zhong Chen, Junmei Wang, and Xiang-Qun Xie J. Chem. Inf. Model., 47 (4), 1626 -1637, (2007)
	*Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations* Patrick Maass, Tanja Schulz-Gasch, Martin Stahl, and Matthias Rarey J. Chem. Inf. Model., 47 (2), 390 -399, (2007)
	*Supervised Scoring Models with Docked Ligand Conformations for Structure-Based Virtual Screening* Reiji Teramoto and Hiroaki Fukunishi J. Chem. Inf. Model., 47 (5), 1858 -1867, (2007)

	*From Modeling to Medicinal Chemistry: Automatic Generation of Two-Dimensional Complex Diagrams* Katrin Stierand and Matthias Rarey Chem. Med. Chem., 2 (6), 853 - 860 (2007)
	*Chemical Fragment Spaces for de novo Design* Harald Mauser and Martin Stahl J. Chem. Inf. Model., 47 (2), 318-324 (2007)
	*Homology Modeling of Human Fyn Kinase Structure: Discovery of Rosmarinic Acid as a New Fyn Kinase Inhibitor and in Silico Study of Its Possible Binding Modes* Dubravko Jelic, Boris Mildner, Sanja Kostrun, Krunoslav Nujic, Donatella Verbanac, Ognjen Culic, Roberto Antolovic, and Wolfgang Brandt J. Med. Chem., 50 (6), 1090-1100 (2007)

	*Interpretation of Scoring Functions Using 3D Molecular Fields. Mapping the Diacyl-Hydrazine-Binding Pocket of an Insect Ecdysone Receptor* B. Bordas, I. Belai, A. Lopata, and Z. Szanto J. Chem. Inf. Model., 47 (1), 176-185 (2007)
	*A Structure-Based 3D-QSAR(CoMSIA) Study on a Series of Aryl Diketoacids (ADK) as Inhibitors of HCV RNA-dependent RNA Polymerase* J. Kim, J. H. Han, and Y. Chong Bull. Korean Chem. Soc. 27, 11, 1919-1922 (2006)
	*Docking studies of agonists and antagonists suggest an activation pathway of the A₃ adenosine receptor* S. Kim, Z. Gao , L. S. Jeong , and K.A. Jacobson J. Mol. Graph. Model. 25 (4), 562-577 (2006)

	*FlexNovo: structure-based searching in large fragment spaces.* J. Degen, M. Rarey Chem. Med. Chem., 1(8), 854-68 (2006)
	*Prediction of Multiple Binding Modes of the CDK2 Inhibitors, Anilinopyrazoles, Using the Automated Docking Programs GOLD, FlexX, and LigandFit: An Evaluation of Performance.* H. Sato, L. M. Shewchuk, and J. Tang J. Chem. Inf. Model., ASAP article
	*Virtual Screening for beta-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228.* T. Polgár and G. M. Keserü J. Med. Chem., 48, 3749-3755 (2005)

	*New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies.* Dhilon S. Patel and Prasad V. Bharatam J. Comput.-Aided Mol. Des. 20, 55-66 (2006)
	*Current Status of Virtual Screening as Analysed by Target Class.* Martin J. Stoermer Med. Chem. 2, 89-112 (2006)
	*Successful computer guided planned synthesis of (4R)-thiazolidine carboxylic acid and its 2-substituted analogues as urease inhibitors.* KM Khan et. al. Mol. Divers. 10, 223-231 (2006)

	*Ligand Selectivity for the Acetylcholine Binding Site of the Rat α5β2 and α3β4 Nicotinic Subtypes Investigated by Molecular Docking* Bisson, W. H.; Scapozza, L.; Westera, G.; Mu, L.; Schubiger, P. A J.Med.Chem, 48, 5123-5130 (2005)
	*In silico fragment-based discovery of DPP-IV S1 pocket binders* Rummey, C.; Nordhoff, S.; Thiemann, M.; Metz, G. Bioorg Med Chem Lett, 16(5), 1405-1409 (2006)
	*Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols* Guichou, J.-F.; Viaud, J.; Mettling, C.; Subra, G; Lin, Y.-L.; Chavanieu, A. J. Med. Chem. 48 (17), 5448-5465 (2005)

	*A Critical Assessment of Docking Programs and Scoring Functions* G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, and M. S. Head J. Med. Chem. 49 (20) 5912-5931 (2006)
	*Improved FlexX Docking Using FlexS Determined Base Fragment Placement* S. S. Cross J. Chem. Inf. Model. 45, 993-1001 (2005)
	*Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols* A. Evers, G. Hessler, H. Matter, and T. Klabunde J. Med. Chem. 48 (17), 5448-5465 (2005)

	*Virtual Screening in Drug Discovery* J. Alvarez and B. Shoichet (Eds)
	*Design of Small-Sized Libraries by Combinatorial Assembly of Linkers and Functional Groups to a given Scaffold: Application to the Structure-Based Optimization of a Phosphodiesterase 4 Inhibitor* M. Krier, J.X. de Araújo-Júnior, M. Schmitt, J. Duranton, H. Justiano-Basaran, C. Lugnier, J.-J. Bourguignon, and D. Rognan J. Med. Chem. 48 (11), 3816-3822 (2005)
	*Virtual docking approaches to Protein kinase B inhibition* M. Forino, D. Jung, J.B. Easton, P.J. Houghton, and M. Pellechia J. Med. Chem. 48 (7), 2278-2281 (2005)

	*FlexX-Scan: Fast Structure-Based Virtual Screening* I. Schellhammer and M. Rarey PROTEINS: Structure, Function, and Genetics 57, 504-517 (2004)
	*Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results* A.E. Klon, M. Glick, and J.W. Davies J. Med. Chem.; (Letter), 47 (18), 4356-4359 (2004)
	*Virtual Screening: finding needles in a haystack on a shoestring* D.E. Clark, N.V. Harris, A.G. Roach, and A.D. Baxter Drug Discovery World 2, 37-41, (2004)

	*Identification of Compounds with Nanomolar Binding Affinity for Checkpoint Kinase-1 Using Knowledge-Based Virtual Screening* P.D. Lyne, P.W. Kenny, D.A. Cosgrove, C. Deng, S. Zabludoff, J.J. Wendoloski, and S. Ashwell J. Med. Chem. 47, 1962-1968 (2004)
	*Identifying the binding mode of a molecular scaffold* D. Chema, D. Eren, A. Yayon, A. Goldblum, and A. Zaliani J. Comput. Aided. Mol. Des. 18, 23-40 (2004)
	*Automated Drawing of Structural Molecular Formulas under Constraints* P. Fricker, M. Gastreich, and M. Rarey J. Chem. Inf. Comput. Sci. 44, 1065-1078 (2004)

	*Novel technologies for virtual screening* T. Lengauer, C. Lemmen, M. Rarey and M. Zimmermann Drug Discovery Today 9 (1), 27-34 (2004)
	*The FlexX Database Docking Environment - Rational Extraction of Receptor Based Pharmacophores* H. Claussen, M. Gastreich, V. Apelt, J. Greene, S.A. Hindle, and C. Lemmen Current Drug Discovery Technologies 1, 49-60 (2004)
	*Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier* A. Bender, H.Y. Mussa, R.C. Glen and S. Reiling J. Chem. Inf. Comput. Sci. 44, 170-178 (2004)

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