March 2006 Volume 1, Issue 3 Bioinformatics

The View from Here John Wooley Bioinformatics in drug discovery: knowledge management via the integration of multiscale, multimodal information... Read more... Upcoming Issues Issue 4/April'06 Cancer Therapeutics Issue 5/May'06 Gene Expression Profiling Issue 6/June'06 Imaging Editor's Choice Sign Up for email Update your details Unsubscribe Contact Us

Drug Discovery Today    Latest issue    home       Top Reviews Optimizing the use of open-source software applications in drug discovery Geldenhuys, W.J. et al Drug Discovery Today Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Representativity of target families in the Protein Data Bank: impact for family-directed structure-based drug discovery Mestres, J. Drug Discovery Today Analysis of the population of enzyme structures in the Protein Data Bank across all levels of the functional classification based on enzyme commission (EC) numbers reveals that, in spite of the almost exponential growth in the number of structures deposited, progress in achieving complete occupancy at all EC levels is relatively slow... Improving the hit-to-lead process: data-driven assessment of drug-like and lead-like screening hits Wunberg, T. et al Drug Discovery Today Drug-like and lead-like hits derived from HTS campaigns provide good starting points for lead optimization. However, too strong emphasis on potency as hit-selection parameter might hamper the success of such projects. A detailed absorption, distribution, metabolism, excretion and toxicology (ADME-Tox) profiling is needed to help identify hits with a minimum number of (known) liabilities... Click here to subscribe to to Drug Discovery Today.   PharmaDiscovery - An Elsevier Event 10-12th May 2006, Bethesda, Maryland Featured session: Innovation around the use of information and applied knowledge CHAIR: Eric Neumann, Director of the Clinical Semantics Group, W3C Click here to download the conference brochure and/or register.   Abstracts of Key Research Papers Catalyzing Inquiry at the Interface between Computing and Biology, NRC Study J.C. Wooley and H.S. Lin, eds National Research Council of the National Academies Pocketome via comprehensive identification and classification of ligand binding envelopes J. An, M. Totrov, R.J. Abagyan Mol Cell Proteomics. 2005 Jun;4(6):752-61. Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions C.J. Camacho, H. Ma, P.C. Champ Proteins. 2006 Feb 27; Epub Representing receptor flexibility in ligand docking through relevant normal modes C.N. Cavasotto, J.A. Kovacs, R.A. Abagyan J Am Chem Soc. 2005 Jul 6;127(26):9632-40. On evaluating molecular-docking methods for pose prediction and enrichment factors H. Chen et al J Chem Inf Model. 2006 Jan-Feb;46(1):401-15. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules D. Hamelberg, J. Mongan, J.A. McCammon J Chem Phys. 2004 Jun 22;120(24):11919-29. VX-680, a potent and selective small-molecule inhibitor of the Aurora kinases, suppresses tumor growth in vivo E.A. Harrington et al Nat Med. 2004 Mar;10(3):262-7. Epub 2004 Feb 22. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures R. Mendez et al Proteins. 2005 Aug 1;60(2):150-69. Target flexibility in molecular recognition J.A. McCammon Biochim Biophys Acta. 2005 Dec 30;1754(1-2):221-4. Epub 2005 Sep 12. A critical assessment of docking programs and scoring functions Gregory L. Warren et al J. Med. Chem. 2005 ASAP Article; DOI: 10.1021/jm050362n.

Drug Discovery Today Subscribe Now! Read journal on ScienceDirect RELATED CONFERENCES PharmaDiscovery 2006 SCIpharm 2006 7th International Oracle Life Sciences User Group Meeting RELATED JOBS Structural biologists D. E. Shaw research, LLC, New York [more details] Genomic standards consortium programmer Centre for ecology & hydrology, Oxford, UK [more details] Meddra coding specialist Genzyme, Cambridge, Massachusetts [more details]