Paper: myChEMBL - a virtual machine implementation of open data and cheminformatic tools

We have just had a paper published in Bioinformatics on myChEMBL - the Linux VM that contains a fully functional version of the ChEMBL database. The paper is here.



myChEMBL is available for download at:



ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current



A warning, it is a fairly big download (ca. 18GB, so try and do this over a fast stable connection)



Source code is available here:

https://github.com/rochoa85/myChEMBL

%T myChEMBL: A virtual machine implementation of open data andcheminformatics tools
%J Bioinformatics
%D 2013
%O DOI:10.1093/bioinformatics/btt666
%A M. Davies
%A G. Papadatos
%A F. Atkinson
%A J.P. Overington

Paper: The ChEMBL bioactivity database: an update

An update to what has happen to the Wellcome Trust funded database ChEMBL over the past few years has just been published - it seems odd, that we've been around long enough to achieve our 2nd NAR Database paper - so much more to do though! This paper contains features and content up to ChEMBL 17.



This could put you in a difficult position which NAR paper to cite in your own publications using ChEMBL; so we suggest both! ;)



Oh, and it's Open Access, of course.

%J Nucleic Acids Research
%D 2013
%P 1–8 
%O doi:10.1093/nar/gkt1031
%T The ChEMBL bioactivity database: an update
%A A.P. Bento
%A A. Gaulton
%A Anne Hersey
%A L.J. Bellis,
%A J. Chambers
%A M. Davies
%A F.A. Krueger
%A Y. Light
%A L. Mak
%A S. McGlinchey
%A M. Nowotka
%A G. Papadatos 
%A R. Santos
%A J.P. Overington

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Paper: The Functional Therapeutic Chemical Classification System

Here's an Open Access paper from Samuel in the group.



Drug repositioning is the discovery of new indications
for compounds that have already been approved and used in a
clinical setting. Recently, some computational approaches have been
suggested to unveil new opportunities in a systematic fashion, by
taking into consideration gene expression signatures or chemical
features for instance. We present here a novel method based on
knowledge integration using semantic technologies, to capture the
functional role of approved chemical compounds.



In order to computationally generate repositioning
hypotheses, we used the Web Ontology Language (OWL) to formally
define the semantics of over 20,000 terms with axioms to correctly
denote various modes of action (MoA). Based on an integration
of public data, we have automatically assigned over a thousand
of approved drugs into these MoA categories. The resulting new research resource is called the Functional Therapeutic Chemical Classification
System (FTC) and was further evaluated against the content of the
traditional Anatomical Therapeutic Chemical Classification System
(ATC). We illustrate how the new classification can be used to
generate drug repurposing hypotheses, using Alzheimers disease as
a use-case.


A web application built on the top of the resource is
freely available at https://www.ebi.ac.uk/chembl/ftc. The source code
of the project is available at https://github.com/loopasam/ftc. 

%T The Functional Therapeutic Chemical Classification System
%D 2013
%J Bioinformatics
%A S. Croset
%A J.P. Overington
%A D. Rebholz-Schuhmann

%O Open Access

Paper: Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

Here's a paper detailing some multi-method target prediction work as part of the GeMoA FP7 project. Proud, as ever, to publish Open Access.

%A Martínez-Jiménez F
%A Papadatos G
%A Yang L
%A Wallace IM
%A Kumar V
%A Pieper U
%A Sali A
%A Brown JR
%A Overington JP
%A Marti-Renom MA
%D 2013 
%T Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis
%J PLoS. Comput. Biol. 
%V 9
%P e1003253
%O doi:10.1371/journal.pcbi.1003253

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Congratulations to Ben Stauch PhD!

Ben Stauch in the group has just been examined on his these - 'Methods for the Investigation of Protein-Ligand Complexes'. This was a tour de force of many techniques - NMR, computational and X-ray crystallography. Ben will be around for a few more months, writing things up, and completing/starting some experimental work on Xe complex refinement and characterisation.



Congratulations to Ben from all the group!



In due course, the thesis will be downloadable from the EBI and EMBL websites, and I'll update this post when the files are there.



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Document Similarity in ChEMBL - 2

Following up on yesterdays post by George and Mark, I put together a slide, hopefully illustrating the advantages of document comparison using objects other than words alone.

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Paper: Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

A paper from Gerard in the group on some of his proteochemometric modelling work; a link to the paper is here. Z-scales rule! (the original Sandberg et al J Med Chem paper on the Z-scales was one of my 'lightbulb turning on' moments in my professional life - go hunt it down if you don't know it.)

%T Benchmarking of protein descriptor sets in proteochemometric modeling (part 2: modeling performance of 13 amino acid descriptor sets
%A G.J.P. van Westen
%A R.F. Swier
%A I. Cortes-Ciriano
%A J.K. Wegner
%A J.P Overington
%A A.P. IJzerman
%A H.W.T. van Vlijmen
%A A. Bender
%J J. Cheminformatics 
%D 2013
%V 5
%O doi:10.1186/1758-2946-5-42

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