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Welcome to the 11th edition of the BioSolveIT newsletter
In our newsletter we publish information about new developments, events, milestones, and scientific facts on a quarterly basis. To download the full printable version, please click here.
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| FlexNovo |
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FlexNovo is a new software tool developed by Joerg Degen and Matthias Rarey at the Center of Bioinformatics, University of Hamburg. It permits structure-based searching within large chemical fragment spaces, concatenating together the fragments according to certain rules that specify how these fragments can be connected. Like its sibling FlexX, it consists of an incremental construction algorithm. During the build-up process, several filters (Lipinski, pose-geometry, diversity) can be activated. The software has been tested on four different targets DHFR, CDK2, COX-2, and ER and has shown very promising results. FlexNovo generated diverse sets of molecules that are highly complementary to the binding site of the protein and that exhibit structural motifs of the binding modes of known actives. For the original publication, please take a look here and for additional information on FlexNovo from Hamburg University please take a look here. FlexNovo is available for beta testing. Please contact us either through our support page or via e-mail at FlexNovo@BioSolveIT.de.
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| better, faster, more: the new FlexX Release 2.1 |
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FlexX Release 2.1 is the latest edition of the well established and popular FlexX protein-ligand docking tool. The software is supported on Linux, MS Windows, SGI Irix; we also have a significantly faster 64 bit Linux version available; additional operating systems are available on request. FlexX 2.1 now supports very large input/output files to allow millions of ligands in libraries to be handled with ease. The software can be accessed from the familiar molecular modeling environments of SYBYL® and MOE®. The new MOE-FlexX interface combines the strengths of MOE's data preparation and results analysis capabilities with FlexX's fast precise docking calculations. FlexX-Screen is a new module for rapidly screening vast corporate compound libraries at less than 1 second per compound with no loss in accuracy compared to standard FlexX. In addition, the module also contains many different customizable filters for toxicity, reactivity and drug-likeness (Lipinski). If you are interested in evaluating the new FlexX, please write to FlexX@BioSolveIT.de or visit our web page.
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| FlexX is going graphical: a new GUI for structure-based drug design |
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BioSolveIT will soon be proud to present FlexX in its newest clothes. Preparing receptor description files, editing config.dat files will soon belong in the past. The avid modeler will only need to start the program and will be guided by FlexX's intuitive graphical user interface workflow. From receptor and ligand preparation — alternate locations of amino acid side-chains, protonation in the active site, ligand initialization and removal of ambiguities — can now be handled automatically, but of course still allowing the user the possibility to tweak specifically desired parameters within the GUI. Here are a couple of sample screen shots.
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| CoLibri |
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CoLibiri is a library design tool conceptualized and implemented in conjunction with Pfizer and Boehringer Ingelheim. The tool has been designed for intricate compound handling during virtual screening experiments. Vast compound collections can be assembled from multiple sources containing various different input formats whilst removing duplicates. Assessing distributions of physico-chemical properties of compounds, chemically selecting/filtering based on property thresholds, molecular name-patterns or absence/presence of a particular substructure motif can be achieved effortlessly. In addition, CoLibiri can be used to create fragment libraries in two ways. Firstly ligands are decomposed into fragment libraries, which can then follow customizable retrosynthetic ligand reconstruction to form a library of novel molecules. Secondly, multiple combinatorial libraries can be assembled into non-redundant fragment combi-chem spaces. Fragment spaces have the advantage of covering a large area of chemical space with only a small number of fragments and can be used with FTrees-FS and FlexNovo. CoLibiri version 1.0 will be shortly available for download. If you would like to evaluate CoLibiri, lease the software from us or have any questions relating to CoLibiri please don't hesitate in contacting us either through our support page or via e-mail at CoLibri@BioSolveIT.de.
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| tips and tricks from the world of FlexX |
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This section focuses on troubleshooting and aspects of FlexX that are either not very well known or are sometimes misunderstood, so we see them as important points to bring to your attention. In this issue we will focus on protein-ligand clash treatment in FlexX. Read more!
You can view previous topics of tips and tricks here. If you have any questions or know of any tips and tricks yourself that you would like to share with the FlexX user community, we would appreciate your input either through our support page or via e-mail at FlexX@BioSolveIT.de.
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| BioSolveIT news in brief |
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Dates for your diary: BioSolveIT will be present at the following conferences:
If you would like to meet a representative of BioSolveIT to discuss any questions or have any kind of feedback please email us at Contact@BioSolveIT.de.
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| literature corner |
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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)
details here
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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)
details here
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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)
details here
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| upcoming articles |
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The New FlexX GUI: Hassle Free Docking |
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FTrees-XL: The Latest Graphical Interface for FTrees |
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FlexX and FTrees in Pipeline Pilot |
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