The ChEMBL-og

Last year, MMV released the MMV Malaria Box , a physical set of 400 probe- and drug-like compounds with confirmed anti-malarial activity. The 'Box' has been since distributed to a large number of academic labs around the world, where the compounds are screened against other plasmodia strains and pathogens such as schistosoma and mTB. The assay results have started coming back in the form of data depositions and, we, as MMV partners, are doing our best to integrate them with both the malaria-data database, as well as the main ChEMBL one. Recent examples of such MMV Malaria Box screening data depositions include: An mTB screen by the Nathan lab in Cornell A schistosoma screen by  Conor Caffrey  and colleagues in UCSF A  plasmodium apicoplast screen by the Derisi lab in UCSF, as reported in our post last week In addition, we curate and integrate the bioactivity data produced by the excellent  Open Source Malaria project. The value of shari...

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

Some of our collaborators at the Karolinska have a great job available - the advert is here . Division Chemical Biology Consortium Sweden (CBCS) are looking for a highly motivated and talented Cheminformatics Scientist to support and coordinate a wide scope of research informatics applications and data analysis at our Stockholm facilities. Duties The desired candidate will have a demonstrated track record in managing large volumes of scientific data in support of basic research and/or drug discovery projects and should have significant experience with in-house and commercial software solutions that facilitate data capture, analysis and visualization in small molecule research and drug design. Responsibilities include: Evaluation and implementation of a nationally encompassing chemoinformatics system for the SciLifeLab community. Maintainance, configuration, monitoring, and/or troubleshooting scientific applications and underlying software.  Partnering and interaction ...

Teach-Discover-Treat (TDT) is excited to announce our 2014 Competition. We have four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility. Three cash prizes - plus partial reimbursement of travel - will be awarded! Winners are required to present their work at the TDT Award symposium during the Fall 2014 ACS National Meeting in San Francisco, California. Create and submit computational workflows that inspire drug discovery activities using freely available software tools. Detailed informationabout the 2014 Competition can be found here:  http://www.TDTproject.org/ 2014-competition.html Submissions deadline is  February 3, 2014 . The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito @TeachDiscoTreat

ATC Code: Wikipedia: Ibrutinib On November 13, 2013, the FDA approved Ibrutinib (Imbruvica TM ) for the treatment of patients with mantle cell lymphoma (MCL) who have received at least one prior therapy. MCL is a subtype of B-cell lymphoma and accounts for 6% of non-Hodgkin's lymphoma cases. In an open-label, multi-center, single-arm trial of 111 previously treated patients, Ibrutinib showed a 65.8% response rate. Ibrutinib is an irreversible inhibitor of the Tyrosine-protein kinase BTK (Uniprot:Q06187; ChEMBL: CHEMBL5251 ; canSAR target synopsis ) and is the first approved targeted BTK inhibitor. It forms a covalent bond with a cysteine residue via a Michael acceptor mechanism, in the BTK active site, leading to inhibition of BTK enzymatic activity Ibrutinib (ChEMBL: CHEMBL1873475 ; canSAR drug synopsis ; also known as CRA-032765 and PCI-32765) has the formula C25H24N6O2 and a molecular weight 440.50. It is absorbed after oral administration with a median Tma...

ATC Code:  L01XC15 Wikipedia: Obinutuzumab On November 1, 2013 the FDA approved obinutuzumab (Gazyva TM ) for use in combination with chlorambucil  (a nitrogen mustard alkylating agent) for the treatment of patients with previously untreated chronic lymphocytic leukemia (CLL). CLL is the most common type of Leukaemia accounting for 35% of all reported Leukaemias (See CRUK CLL page). In a randomized three-arm clinical study, the combination of obinutuzumab (in combination with chlorambucil) improved the progression-free survival (PFS) of patients to 23.0 months compared to 11.1 months for chlorambucil alone. Obinutuzumab ( CHEMBL1743048 ) is a humanized anti-CD20 monoclonal antibody of ca . 150 kDa molecular weight. Its target, the B-lymphicyte antigen CD20, is the product of the gene MS4A1 (Uniprot: P11836; ChEMBL: CHEMBL2058 ; canSAR target synopsis . The CD20 antigen is expressed on the surface of pre B- and mature B-lymphocytes. Obinutuzumab mediates B-ce...

We are very pleased to announce the release of two new datasets on the ChEMBL-NTD portal. The first dataset is provided by the Drug for Neglected Diseases initiative (DNDi) and is focused on the selection and optimization of hits from a high-throughput phenotypic screen against Trypanosoma cruzi . The paper describing the dataset in more detail can be accessed here and the data can be downloaded from here .   The second dataset from the DeRisi Lab UCSF and is focused on the screening of MMVs Malaria Box compounds in Plasmodium falciparum , to understand if anti-malarial compounds target the apicoplast organelle. More details about the dataset can be found here and the data can be downloaded from here .   Both datasets will be loaded into the next version of ChEMBL, which will be due out early next year. The ChEMBL - Neglected Tropical Disease portal is a repository for Open Access primary screening and medicinal chemistry data directed at neglected diseases. ...