December 2010 Update

Welcome to our December Computational Chemistry Update! This newsletter aims to provide an overview of some interesting developments in the computational chemistry field as well as listing some conferences & meetings which may be of interest to the modelling community, together with some jobs available. We would welcome any ideas for future articles, conferences, job postings and feedback so we can ensure the content of future editions is timely and informative.

In this issue we have articles on Knime, the new release of MOE from CCG, plus conference listings and job listings.

Data Pipelining with KNIME: Power to the People!

Data pipelining has been around for some time, but – judging by the starring role it has been assuming at several recent chemoinformatics & modelling meetings – it now seems to be firmly established at the forefront of many leading R&D organisations as the method of choice for disseminating predictive computational tools to scientists.

Pipelining brings applications from multiple sources into a single graphical interface, allowing chemists and biologists to regain control of property calculations, data analysis, selection of compounds for purchase, docking studies, predictive ADMET approaches….basically any task which can be performed computationally. And this seems to be going down a treat with the scientists. Mike Bodkin (Lilly) presented a talk at the Autumn UK QSAR & Chemoinformatics Group meeting at the EBI, Hinxton, where he described how widely and enthusiastically pipelining tools have been embraced at Lilly. The chemists routinely use the workflows compiled by the chemoinformatics/modelling groups, and the modellers often assume a “consultancy” role, assisting the chemists as they use the tools, and modifying the tools as needed by the chemists.


Whilst commercial pipelining options are available, such as Pipeline Pilot from Accelrys, the open-source KNIME system ( offers an excellent framework for pipelining, and many modelling software vendors now supply ready-made KNIME nodes to complement the functionality already offered through the system. KNIME comes with many nodes specific to chemical applications (eg SDF & mol2 file input & output, fingerprint creation, molecule sketcher, statistical methods) and these are complemented by the Weka nodes also distributed with KNIME which offer classification tools such as clustering & Bayesian algorithms.

Pipelining lets you pull together your chosen software tools into a user-friendly graphical tool which can be accessed by any scientist in your organisation.

For more information on pipelining with KNIME or to discuss development of tailor-made KNIME workflows contact Susan Boyd at CompChem Solutions.

New MOE Release – MOE 2010.10

In the year that brought us Avatar in glorious 3D, CCG have now released their new 3D stereo version of MOE, which comes complete with its own set of 3D viewing glasses. Don’t try to watch Avatar wearing them though as it’s kind of a different system….! As well as the new mode for 3D viewing, the MOE graphics have been enhanced and accelerated throughout.

MOE 2010

The interface looks a little different too. CCG have worked closely with their clients over the last year to optimise the new interface which has been redesigned for ease-of-use.

One key new feature of the 2010 release is the kinase database browser & explorer. Over 2000 protein kinase crystal structures from the PDB have been aligned, and users can query the structure database very flexibly, based on ligand topology, receptor domain information, residues in the active site and activation state, for example.

A new NAMD interface is now in place, enabling large-scale molecular dynamics simulations to be set-up within the MOE environment.

For modellers supporting medicinal chemistry projects, the new methodology to perform rule-based medicinal chemistry transformations on structures which are docked into a receptor pocket should be of interest. Pharmacophore, synthetic tractability and physchem parametric filters can be set-up ahead of the computation to ensure that the compounds suggested are in line with expectations.

All in all the new package has been developed with the needs of MOE’s users in mind. Certainly much of the new functionality will be of interest to us at CompChem Solutions.

For more information on how CompChem Solutions can help your modelling efforts using the new MOE system, contact Susan Boyd at CompChem Solutions.

Upcoming Meetings

One Nucleus Europe-Wide Scientific Poster Day, 18 January 2011, Granta Park Nr Cambridge,

Peter Murray Rust Symposium, 17 January 2011, University of Cambridge Contact Andreas Bender for more information

RSC Antibiotics- Where now?, 20 January 2011, Burlington House,

Cambridge Chemoinformatics Network Meeting, Q1 2011 Contact Andreas Bender ( for more information

SMI Advances & Progress in Drug design, London, 21-22 Feb 2011,

RSC Fragments, GSK Stevenage, 7-8 March 2011,

MGMS Membrane Proteins: Structure & Function, 6-8 April 2011, Oxford

UK QSAR & Chemoinformatics Group Spring Meeting, late Spring 2011, Manchester

9th International Conference on Chemical Structures, 5-9 June 2011, Noordwijkerhout, The Netherlands

The above list is not exhaustive, but constitutes a set of meetings which may be of interest to computational chemists & chemoinformaticians. If you have an upcoming meeting you’d like us to include in our spring newsletter please contact Susan Boyd.

Positions Open

Senior Computational Chemist, Biofocus, Gt Chesterford,

Software engineer, Technical support engineer & German-speaking Inside sales representative, Accelrys (UK),

Statistician/bioinformatician, Evotec, Germany,

Bioinformatician (Ensemble genomes), EBI Hinxton, Nr Cambridge, job ref EBI_00047

Bioinformatician (EU openscreen), EBI Hinxton, Nr Cambridge, job ref EBI_00055

Academic Account manager, Europe, Schrodinger Inc,

Technical support specialist, Mannheim, Germany, Schrodinger Inc,

PhD position at the Institute for Cancer Research,

Post-doc in computational chemistry, Inhibox, Oxford,

Senior application scientist in computational chemistry, Inhibox, Oxford,

PhD Studentship University of Bradford/CCDC

Research Fellow in biostatistics, Brunel University, West London,

Teaching Associate in Computational Chemistry, University of Nottingham,

Post-doc scientist: Modelling the antibody, UCB, Slough, job ref SLO00001610

Pharmacometric /modelling & simulation, inflammation and immunology specialist, UCB, Belgium & Slough, job ref BRA00002379

Marie Curie Research Fellow, Dept of Physics, University of Strathclyde, 2 yrs Glasgow, 1 yr Gothenburg,

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.

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