In this issue we have articles on StarDrop which can accelerate drug discovery through predictive ADMET property prediction, some applications of computational biology, some news, some job vacancies within the modelling community in general, some upcoming meetings of interest to computational chemists and details of our Summer Special Offer.
Born many moons ago, when Inpharmatica was still high in the sky, StarDrop has now grown into a stellar suite of software to aid drug discovery.
Biofocus spin-out Optibrium have been developing the software since 2003, and they have designed the interface with chemists very much in mind.
StarDrop has been developed to help scientists find novel molecules with the required balance of properties to become drug development candidates. StarDrop brings together a variety of computational methods for generating in silico models and analysing data in a user- friendly environment, making it simple to handle uncertainty in the data. One notable innovation is the ‘glowing molecule’ graphic which highlights dynamically the influence of each atom on the modelled properties, allowing medicinal chemists to immediately see the effect of structural changes, and to modify structures whilst monitoring the effects on properties.
The ADMET QSAR plug-in enables calculation of additional properties such as BBB penetration, hERG, P-gp transportation, logD, human intestinal absorption and p450 propensity, although the p450 Metabolism plug-in will predict likely metabolism in much more detail.
The software also comes with tools for diversity assessment and selection, and can be linked with other installed software systems to allow integration with multiple data sources for additional model building and/or visualisation.
Using StarVue, a free molecular visualiser from Optibrium, scientists can share their StarDrop results with others who have no access to the full interface.
CompChem Solutions has recently entered into a collaboration with Optibrium, and is now able to access StarDrop to assist research projects for clients. The software very nicely complements the excellent range of software already accessible to CompChem Solutions, and expands our capabilities in the ADMET prediction area.
For more information on StarDrop see http://www.optibrium.com/stardrop.
Computational biology means many things to many people. I have heard people use the term when referring to biological database management, systems biology, sequence comparison and microarray database analysis. A pretty diverse array of topics I’d say. I think the general consensus, however, is that computational biology attempts to make sense of biological systems.
In terms of new target identification, microarray database analysis must surely be one of the most useful innovations in recent years. Oncomine, for example, now contains over 600,000 sample facts on more than 43k oncology samples, and is available for comparison of gene expression profiles and filtering for “druggable” targets such as kinases. Biological pathway identification, association of diseases with the gene signature of a compound, and identification of pathways regulated by a compound can also be facilitated by use of the database.
Beyond oncology, the MetaCore pathway database from GeneGo contains information on around 4,500 genes, with “causal” gene-disease associations for over 500 human diseases. The system is well set up to aid drug target selection and validation, biomarker identification and patient profiling in clinical trials.
These approaches have already proven their worth in target identification. Indeed, three independent studies using Oncomine have identified SOX2 as the target of recurrent amplification in the 3q26-3q28 chromosomal region associated with squamous cell carcinoma (Nat Genet. 2009 Nov;41(11):1238-42, PLoS One. 2010 Jan 29;5(1):e8960, PLoS One. 2010 Feb 9;5(2):e9112).
With the current drive to identify ever more novel targets, surely the future of target identification will be rooted in computational biology.
For more information on how CompChem Solutions can help with target identification and other applications using computational biology, contact Susan Boyd.
Susan Boyd of CompChem Solutions is delighted have joined the organising committee of the UK QSAR & Chemoinformatics Group. The group arranges two meetings annually, covering a range of topics relevant to computational medicinal chemistry. If you would be interested in speaking or presenting a poster at a future meeting, would like to host a meeting or have some suggestions for future topics of interest, please contact Susan Boyd.
CompChem Solutions has worked with many diverse clients over the years. This summer, as part of our expanding business model, we’d like to extend an offer to some of you who we’ve not yet met. We’re so confident you’ll be pleased with our services that we are offering 2 FREE DAYS of computational chemisty consultancy services to new clients of CompChem Solutions starting a project with us in June, July or August of 2011. Please note that the offer is limited to the first 5 companies taking up the offer, and that all projects undertaken must be of at least 3 days duration. The offer does not apply to any past or present clients of CompChem Solutions.
Quantum Bioinorganic Chemistry QBIC 2011, 25-28 June, Prague, http://www.qbic2011.cz/
Cambridge Chemoinformatics Network Meeting, 29th June 2011 Contact Andreas Bender (email@example.com) for more information
Modelling Interactions in BioMolecules V MIB’11, September 4th-9th 2011, Czech republic,http://physics.mff.cuni.cz/kchfo/MIB11/
“Connecting structure to function: from calculation to experiment and back again”, 19-21 September, 2011, University of Cambridge, symposium in honour of Dr Andy Vinter. Seehttp://www.mgms.org/JGV_meeting/index.html for more information.
22nd International Symposium: Synthesis in Organic Chemistry, 11-14 July 2011, Churchill College, Cambridge, UK, http://www.rsc.org/ConferencesAndEvents/ RSCConferences/OrganicSynthesis2011/index.asp
EMBO|EMBL Symposium, “Structure and Dynamics of Protein Networks”, 13 – 16 October 2011, Heidelberg, Germany, www.embo-embl-symposia.org.
The above list is not exhaustive, but constitutes a set of meetings which may be of interest to computational chemists and chemoinformaticians. If you have an upcoming meeting you’d like us to include in our spring newsletter please contact Susan Boyd.
Senior Computational Chemist, Heptares, Welwyn Garden City, Herts, UK,http://www.heptares.com/uploads/Senior%20Computational%20Chemist.pdf
Computer-Aided Drug Discovery (CADD) Scientist, Novartis, Basel, Switzerland, www.careers.novartis.com, Job ID 82428.
CADD Postdoctoral Position at Novartis in Cambridge, MA USA, http://nibr.com/careers/postdocs.shtml
Computer Scientist, Crop protection (2 year contract), Syngenta R&D, Switzerland, write to firstname.lastname@example.org. Python, SQL, Pipeline pilot/KNIME experience useful.
AZ/CCDC post-doc opportunity in ligand-based design/pharmacophore tools at AZ Alderley Park,https://gs.globalsuccessor.com/fe/tpl_astra04secure.asp? newms=jj&id=57238&newlang=1
AZ post-doc opportunity on predictive modeling, fragment-based QSAR, Alderley Park,https://gs.globalsuccessor.com/fe/tpl_astra04secure.asp? newms=jj&id=57238&newlang=1
Computational Chemist, EPSRC UK National Service for Computational Chemistry Software (NSCCS) at Imperial College London, http://bit.ly/fcpKiD
Bioinformatics Scientist, Biofocus, Leiden, The Netherlands (http://biofocus.com/careers/Scientist-BioinformaticsLEI-019.htm)
Senior molecular modeller, Argenta Discovery Ltd, Harlow, UK, http://www.argentadiscovery.com/careers/current-opps.htm
The above list is not exhaustive, but constitutes a set of positions which may be of interest to computational chemists & chemoinformaticians. CompChem Solutions takes no responsibility for the accuracy of any listing above or the availability of the positions. If you have a vacancy you’d like us to include in our spring newsletter please contact Susan Boyd.