The ChEMBL-og

Gerard and I have just had a News & Views published in Nature Methods - link to the pdf is here . This is a commentary on a paper by Lin et al . which uses metrics derived from pharmacological similarity to cluster proteins - there are some interesting differences between the same proteins clustered by sequence similarity, anyway, here's the N&V and below is the discussed paper (pdf link here ) %A G. Van Westen %A J.P. Overington %D 2013 %T A Ligand’s-Eye View of Protein Similarity %J Nature Methods %V 10 %P 116-117 %O doi:10.1038/nmeth.2339 %A H. Lin %A M.F. Sassano %A B.L. Roth %A B.K. Shoichet %T A pharmacological organization of G protein-coupled receptors %J Nature Methods %V 10 %P 140-146 %D 2013 %O doi:10.1038/nmeth.2324 jpo

We are pleased to announce the release of ChEMBL_15. This version of the database was prepared on 23rd January 2013 and contains: 1,434,432 compound records 1,254,575 compounds (of which 1,251,913 have mol files) 10,509,572 activities 679,259 assays 9,570 targets 48,735 documents 17 activity data sources You can download the data from the ChEMBL ftpsite: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ Please see chembl_15_release_notes.txt for full details of all changes in this release, including important schema changes! Data changes since the last release: We have made several major changes/additions to the data in ChEMBL_15: Incorporation of data from the USP Dictionary of USAN and International Drug Names. Incorporation of monoclonal antibody clinical candidates and sequences. Creation of targets for protein complexes and protein families. Standardisation of activity data and identification of potential issues. Annotation of predicted compo...

ChEMBL_15 will be released this week. As mentioned previously, there will be some major schema changes. For many users, the most significant of these will be: 1) Removal of protein-specific information (e.g., sequences/accessions) from the target_dictionary to a separate 'component_sequences' table. The target_dictionary now includes entries for protein complexes, protein families and other 'group' targets. These then link to their protein components via the target_components table. 2) Removal of the assay2target table. Each assay now links only to a single target (though this target may consist of multiple proteins in the case of a protein complex/family). Information previously included on the assay2target table (tid, confidence_score etc) is now on the assays table. We have provided a diagram and documentation of the new schema on the chembl ftp site: ChEMBL_15 release documentation Please take some time to familiarise yourselves with the changes befor...

For data managers of chemistry resources, the maintenance of structure-based links to other chemistry resources can be a tedious chore. The job is all the more burdensome knowing that your counterparts in other chemistry based-resources are essentially duplicating your efforts, in order to keep their links to your resource updated. In an attempt to remove this duplication of effort, and automate the processes involved, we have developed UniChem ,  and which is described in a recent publication . Getting structure-based links out of UniChem can be achieved either via the web-interface or the web services. For automated updating, using the web-services is often the best choice. The current set of web service methods has been designed to allow users several options for how they might obtain links data. Below are detailed two possibilities. One such option would be to use the following methods: First, query UniChem for all valid src...

Elvitegravir: Cobicistat: ATC Code :   J05AR09 Wikipedia :  Elvitegravir/Cobicistat /Emtricitabine/Tenofovir On August 27, FDA approved the complete regimen for treatment of Human Immunodeficiency Virus -1 ( HIV-1 ) infection in adults who are antiretroviral treatment-naïve. STRIBILD®, combination of a  HIV-1 integrase  strand transfer inhibitor ( INSTI ) -  Elvitegravir , a pharmacokinetic enhancer -  Cobicistat  and two nucleos(t)ide analog HIV-1  Reverse Transcriptase  (RT) inhibitors ( NRTI's ) -  Emtricitabine/Tenofovir disoproxil . Acquired immunodeficiency syndrome ( AIDS ) is a disease of the human  immune system  caused by  HIV  infection, in which progressive failure of the immune system allows life-threatening  opportunistic infections  and  cancers  to thrive. HIV infects and kills vital cells involved in immune system such as  T hel...

Many of the readers of the ChEMBL-og are interested in drug discovery against neglected and rare diseases. One of the great things for us in this field is the opening up of data in this field - there was the almost simultaneous release of primary HTS data from GSK, Novartis & St. Judes in 2011, more recently the results of a GSK HTS for TB. Having this data publicly available, for all, means that many smart people can analyse the data, and of course, pooling data in this way effectively is equivalent to running the assay against a far larger compound set, and allows more powerful cheminformatics analysis to identify chemical series, preliminary SAR, etc . Many of these datasets are available in our ChEMBL-NTD and ChEMBL-Malaria archives - and we know 2013 will be a great year for more data just like this! All these data are available for download, in the exact form as supplied by the depositor, no accounts/passwords, no lock-in to a software infrastructure, with no restrict...

ATC Code: Wikipedia:   Raxibacumab On December 14th 2012 the FDA approved  Raxibacumab for the treatment of inhalation anthrax, a form of anthrax caused by the inhalation of anthrax spores. The drug is also approved to treat inhalation anthrax when alternative therapies are not available or appropriate. Raxibacumab is a 146 kDa monoclonal antibody that is designed to neutralize the toxin secreted by Bacillus Anthracis . The FDA granted raxibacumab fast track designation, priority review, and orphan product designation. Bacillus Anthracis toxin (Anthrax toxin) is a secreted three protein exotoxin. It consists of two enzyme components;  lethal factor (LF, PDB 1PWU ), a bacterial endopeptidase and edema factor (EF, PDB 1PWW ), a bacterial adenylate cyclase. These are combined with one cell-binding protein; protective antigen (PA, PDB 1ACC ). The individual components are non toxic and the combination of the enzyme components with the cell-...