We will be making a regular point of providing you with the latest publications, reports and papers including developments and products from BioSolveIT and its associated owners.

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)

Presented is a description of an automatic 2D-protein-ligand diagram generation method, PoseView. 2D diagrams help in the important task of visualizing protein-ligand complexes. Large numbers of complexes are becoming available and investigating other protein-ligand complexes visually during drug discovery is common. The method permits transparent visualization of contact partners in a complex and supports scientists in the evaluation of structure-based design results. More information and a web-interface to the tool can be found at www.zbh.uni-hamburg.de/poseview.
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Chemical Fragment Spaces for de novo Design
Harald Mauser and Martin Stahl
J. Chem. Inf. Model., 47 (2), 318-324, (2007)

The paper describes the application of FTrees-FS, our de novo solution for searching large conformational spaces with chemical fragments to find similar ligands to an active/s molecule/s. Chemical fragment spaces are explained, these use combinations of molecular fragments with connection rules to maximize the coverage of known druglike chemical space. The study compared diversity-oriented selection based on maximum common substructures and a method biased towards high frequency of occurrence of fragments. The combination of the methods showed to cover a significantly larger portion of druglike chemical space and successfully providing ideas for novel chemical entry points in the design process.
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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)

The article from GSK presents the application of GOLD and FlexX to Fyn tyrosine kinase, a Src-family enzyme involved in T-cell receptor signal transduction. Rosmarinic acid was discovered as a new Fyn kinase inhibitor using immunochemical and the docking methods. Two possible binding modes of rosmarinic acid were evaluated, near to or in the ATP-binding site of kinase domain of Fyn. The paper states that FlexX has better agreement than GOLD with both crystal structures investigated here and in their previous experience with kinase inhibitors.
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