The ChEMBL-og

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We have faced for some time some issues with compound integration with ChEMBL - specifically the loading of compound sets into ChEMBL for cross referencing, between for example, ChEBI, PDBe compounds, etc . The ChEMBL update cycle is relatively slow with respect to some other resources, and there is inevitable thrash with compounds not being present, especially for exciting new data. Without doing something different for compound integration, we were starting to face a scenario where we had a compound table with many millions of compounds without any bioactivity data, and following this the inevitable slowdown in searching, etc . We also had some issues facing us about curation of other people's primary data, changing compound structures, or their rendering, etc . So, we decided to set up an external system to resolve cross-references between various databases. This is a very simple Standard InChI lookup, containing compounds from resources such as ChEMBL, ChEBI, PDBe, Dru...

We have made a couple of minor updates to the ChEMBL widgets, which include: A new widget has been created, which displays the bioactivity results shared between a ChEMBL compound and a ChEMBL target A new scaling parameter allows you to vary the size of the widget A more informative message is provided when widget has no data to display More details can be found here

We're delighted to announce the availability of three distinct new datasets on the ChEMBL-NTD portal , available for download, reuse, etc. These are: Novartis-GNF Malaria Liver Stage dataset (associated with this Science publication) ( Plasmodium falciparum ). DNDi Human African Trypanosomiasis (HAT) dataset ( Trypanosoma brucei ) DNDi Chagas Dataset ( Trypanosoma cruzi ). Further details of the assays and compounds are to be found on the ChEMBL-NTD portal . The data will be integrated and loaded into a future version of ChEMBL, as well as the direct data download links. Once more, we thanks the depositors, DNDi and Novartis-GNF , for their benevolence and commitment to Open Science. The associated publication for the Novartis-GNF dataset is: %T Imaging of Plasmodium Liver Stages to Drive Next-Generation Antimalarial Drug Discovery %A S. Meister %A D.M. Plouffe %A K.L. Kuhen %A G.M.C. Bonamy %A T. Wu %A S.W. Barnes %A S.E. Bopp %A R. Borboa %A A.T...

We are exploring establishing links from the ChEMBL compounds to patents. The implementation can have two basic routes.... Links from the interface to patents (simple and quick to do now we have UniChem). Patent uri's in the database itself (more complex, and more difficult to keep up to date, but arguably more useful). So to help our planning for next year, comments, wishes are most welcome....

ATC code : L01XX02 On November 18, the FDA approved asparaginase from  Erwinia chrysanthemi for the treatment of patient with acute lymphoblastic leukemia (ALL) who have become allergic to the E. coli asparaginase that is conventionally used for the treatment of ALL patients. ALL is a cancer of the white blood cells and can be fatal within weeks from the onset of the disease if it is left untreated. In ALL, there is an unproportional increase in the population of immature white blood cells, which crowd out functional immune cells as well as red blood cells and platelets, and in advanced stages of the disease infiltrate into tissues and organs, most frequently liver, spleen and lymph nodes. The symptoms of ALL in its initial stages are fatigue, anemia, frequent infections and fever as well as breathlessness and prolonged bleeding. ALL is caused by DNA damage and associated with exposure to radiation and cancerogenic chemicals. There are a number of typical chromosoma...

ATC code (partial): S01LA On November 18th 2011, the FDA approved Aflibercept (trade name: Eylea ; Research Code: AVE-0005,  also known as VEGF Trap), a recombinant fusion protein indicated for the treatment of patients with neovascular (wet) age-related macular degeneration (AMD) . AMD is an eye condition which usually occurs in older patients and affects the macula area of the retina, causing loss of vision and eventually blindness. In particular, wet AMD is characterised by an abnormal growth of new blood vessels ( neovascularisation ) behind the retina. This originates from an abnormal activation of angiogenesis, by the vascular endothelial growth factor-A (VEGF-A; ChEMBL: CHEMBL1783 ; Uniprot: P15692 ) and the placenta growth factor (PlGF; ChEMBL: CHEMBL1697671 ; Uniprot: P49763 ), of the vascular endothelial growth factor receptors VEGFR-1 (ChEMBL: CHEMBL1868 ; Uniprot: P17948 ) and VEGFR-2 (ChEMBL: CHEMBL279 ; Uniprot: P35968 ), two receptor tyrosi...