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Showing posts from December, 2013

New Year, New Job? Research Associate in Epidemiology at UCL (ChEMBL related)

As part of a collaboration the ChEMBL group are involved in with UCL, we are looking to appoint to a full time, three-year position in the Genetic Epidemiology Group, Institute of Cardiovascular Science, one of the component institutes of the UCL Faculty of Population Health Sciences.

The appointee will join an exciting programme of work funded by the UCL National Institute of Heath Research Biomedical Research Centre, through its High Impact Award scheme. The appointee will apply bioinformatic expertise to the late stage development of a new high density genotyping array designed to support drug target validation and related drug development issues; co-ordinate deployment of the array in a large consortium of highly-phenotyped cohort studies (the University College-London School of Hygiene-Edinburgh-Bristol consortium); undertake statistical analysis of the data; and play a leading role in writing manuscripts reporting findings arising from this work.

The post is based at UCL, but t…

Conference: CEADD2014 - Modelling water in biological systems, London, March 2014

A one day conference entitled 'Modelling Water in Biological Systems' will be held at the School of Oriental and African Studies (SOAS) in London on Friday, 28 March, 2014. This meeting, organised by the MGMS, is the latest in the 'Cutting Edge Approaches to Drug Design (CEADD)' series.

In recent years, significant progress has been made in probing the role of water molecules in protein-ligand binding.  Hydration is a crucial factor in understanding binding modes, ligand affinities and kinetics.  Modelling tools are becoming available which may offer new insights in this exciting and evolving area of current research. This conference provides a timely overview of some of the main research avenues in this important field.

ChEMBL Web Service Update 4: A Reminder

This post is to remind users of the ChEMBL Web Services that we will soon be changing the backend to use the new ChEMBL API. Since our initial announcement about the changes, which you can read about here, here and here, we have made some more changes and optimisations, which speed up the services significantly.

We thank everyone for feedback to date and urge anyone else who makes use of the ChEMBL Web Services to test the new version. Remember they are simple to test, just use the following temporary base URL and everything should work as if you are using the current live Web Services:



https://www.ebi.ac.uk/chemblws2

We would like to make the change in January, so please get in touch if you have any questions or experience any problems.

Once we have made the technology switch and happy that it is working in the wild as expected, we will be doing a complete review of the functionality offered by the current ChEMBL Web Services. So expected some big changes in 2014.


UniChem: A resource for compound mapping - use in BioMedBridges

Unichem is a simple database and web service for the InChI-based linkage of chemical structures across various resources. It was initially developed under the EU-OPENSCREEN ESFRI as an approach to link screening data from the planned screening collection to other chemistry resources. The development was then extended under the BioMedBridges project - which spans across various Biomedical Sciences (BMS) ESFRIs (such as ELIXIR, BBMRI, etc.)

It's proved to be remarkably useful to us as well, and will be the future home of regularly updated feeds of compound structures from SureChEMBL - and will allow rapid novelty checking of patent structure novelty, across component datasources. A side-effect of this, is of course, that immediately the compounds in any of the BioMedBridge partner ESFRIs immediately have patent data integration. For us, this synergy, and snowball effect of binding resources together using simple open standards is one of the great joys of our work!

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Notes from Rita's Talk Yesterday.

Rita gave a talk on her recent drug target work yesterday on campus, and Jenny Cham took notes; aren't they great?


jpo

SureChEMBL - Chemical Structure Information in Patents

Today we have announced that we are taking over the running of the SureChem system from Digital Science. We have renamed this SureChEMBL to reflect the history and provenance of the technology and engineering, but also to align it with it's new home and future, we like the name, and hope you do. We are delighted that this has happened - Nicko and the team at Digital Science have been great, and the more we have dug in to how it works, the more we have appreciated the design and vision that they had.

If there is one consistent piece of feedback we get about ChEMBL it is in encouraging us to add patent data to what we do. So now we have, but because the data from patents is different in detail from that reported in the published literature, we will keep the databases separate, but closely integrated.

For those of you that are already SureChem users you will be familiar with the functionality and how it works; but for those that weren't SureChEMBL takes feeds of full text patents…