Again xkcd is the source for the cartoon.
Monday, 30 November 2009
Friday, 27 November 2009
<NAME="Romidepsin"> <SMILES="CC=C1C(=O)NC(C(=O)OC2CC(=O)NC(C(=O)NC(CSSCCC=C2)C(=O)N1)C(C)C)C(C)C"> <InChI="InChI=1S/C24H36N4O6S2/c1-6-16-21(30)28-20(14(4)5)24(33)34-15-9-7-8-10-35- 36-12-17(22(31)25-16)26-23(32)19(13(2)3)27-18(29)11-15/h6-7,9,13-15,17,19-20H,8,10- 12H2,1-5H3,(H,25,31)(H,26,32)(H,27,29)(H,28,30)/b9-7+,16-6-/t15-,17-,19-,20+/m1/s1"> <InChIKey="OHRURASPPZQGQM-GCCNXGTGSA-N"> <ChemDraw=Romidepsin.cdx>The manufacturer of Romidepsin is Gloucester Pharmaceuticals, Inc. and the product website is www.istodax.com.
Thursday, 26 November 2009
Wednesday, 25 November 2009
A brief update of the forthcoming TACBAC 2010 conference. The schedule is now online and it looks very, very good (conflict of interest - I am motivated to say that). But really it does! Have a look for yourself if you don't believe me.
The picture above is the top hit for "TACBAC" in google images. TACtical BACon.
Tuesday, 24 November 2009
We are aware that the 27th is over the forthcoming Thanksgiving weekend for our friends located in the United States of America, but we will do a further web-meeting the following week, for those unable to make it on the 27th.
Please, please, please use the above link, it is just too complex (for me) to manage emails with all sorts of titles, content and so forth! Also, it causes confusion (for me) if you forward the access details, and then I get messages, phone calls, smoke signals, etc. about the meeting if we need to change things.
Friday, 20 November 2009
We have received a couple of questions about the 'privacy' of chemical structure searching of our chembldb interface. The root of these questions seems to be 'Is it safe for me to search with a proprietary structure?'. There are probably two components to this - privacy over the route to our servers, and the privacy of the query once it gets on to our site. Basically, we're not interested in what you are searching for, we don't store the queries at all, and have no desire to disclose this sort of data to anyone; however, there are a number of things we could do in the short-term to address some potential corporate/IP concerns.
We would also welcome contact/discussion to help us develop our longer term 'privacy' strategy for chembldb.
The image is from the excellent xkcd.....
There are only two issues with website implementation - 'interface' and 'content'. We have a project here at the EMBL-EBI connected with interface and UI principles, and they have a blog, here is a link to that blog.
Wednesday, 18 November 2009
ChEMBL small molecule-protein interactions are now available in PSI-MI TAB and XML formats, thanks to the Proteomics Services group. This dataset includes ChEMBL interactions identified via binding assays with IC50/Ki/EC50/Kd values below 10uM - just under 500,000 interactions in total (with negative/weaker interactions also included in the XML export).
The data can be accessed via the PSICQUIC project (Proteomics Standards Initiative Common QUery InterfaCe), which provides programmatic access to a wide range of molecular interaction databases via SOAP and REST web services. For example, this URL retrieves all ChEMBL interactions relating to imatinib (Gleevec).
Mail us if you need more info.
Monday, 16 November 2009
Sunday, 15 November 2009
My kids all think I have a really easy life - international travel, 'holidays' all around the world, and they regularly come out with the line 'hard day at the ice-cream factory?' when I say how busy or stressed at work I am. The latest conference we are presenting at does not help, but why oh why do they never hold the conferences I am invited to in somewhere like the Faroe Islands, where the cod fishing is good.
Anyway, we are speaking at Rocky '09, an ISCB conference held in Aspen, CO from 10th to 12th December. It looks a really, really interesting conference. Here is a link to the schedule.
Thursday, 12 November 2009
Well, it looks like the picture above. Kudos to Tim Nugent for the photography and image processing.
Tuesday, 10 November 2009
The latest approval this month, on October 26th, was Ofatumumab (trade name Arzerra). Ofatumumab is a CD20-directed cytolytic monoclonal antibody indicated for the treatment of patients with refractory chronic lymphocytic leukemia (CLL) who have inadequately responded to both Fludarabine and Alemtuzumab. CLL is characterized by an abnormal proliferation of lymphocytes so-called B-cells. B-cells originate in the bone marrow and are involved in fighting infection. In CLL, the DNA of a B-cell is damaged and so it can not produce antibodies in order to fight infection. Moreover, they grow out of control and accumulate in the bone marrow and blood.
Ofatumumab is an IgG1k human monoclonal antibody which binds specifically to both the small and large extracellular loops of CD20. CD20 is a non-glycosylated phosphoprotein expressed on normal B lymphocytes and on B-cell CLL. Since it is not shed from the cell surface, it allows for antibody binding, and when so, it sends a signal across the membrane to control growth and trigger death of certain tumor cells. The Fab domain of Ofatumumab binds to the CD20 molecule, whereas the Fc domain mediates immune effector functions that result in B-cell lysis.
Ofatumumab has a molecular weight of ca. 149 kDa. The dosing is typically 12 doses administered as an initial 300mg dose, followed 1 week later by a 2,000mg dose weekly for 7 doses, followed 4 weeks later by a further 2,000 mg every 4 weeks for 4 doses (a 2g dose is equivalent to ca. 134umol). It has a volume of distribution ranging from 1.7 L to 5.1 L and its elimination occurs through both a target-independent route and a B-cell mediated route. Ofatumumab clearance is approximately 0.01 L/hr and mean half-life is ca. 14 days. The recommended dosage and full prescribing information can be found here.
<CHEMBL_DRUG> <DRUG_NAME="Ofatumumab" TRADEMARK_NAME="Arzerra"> <DRUG_TARGET UNIPROT="P11836" TARGET_NAME="CD20"> MTTPRNSVNGTFPAEPMKGPIAMQSGPKPLFRRMSSLVGPTQSFFMRESKTLGAVQIMNG LFHIALGGLLMIPAGIYAPICVTVWYPLWGGIMYIISGSLLAATEKNSRKCLVKGKMIMN SLSLFAAISGMILSIMDILNIKISHFLKMESLNFIRAHTPYINIYNCEPANPSEKNSPST QYCYSIQSLFLGILSVMLIFAFFQELVIAGIVENEWKRTCSRPKSNIVLLSAEEKKEQTI EIKEEVVGLTETSSQPKNEEDIEIIPIQEEEEEETETNFPEPPQDQESSPIENDSSP </DRUG_TARGET> </DRUG> </CHEMBL_DRUG>The license holder is GlaxoSmithKline and the product website is www.arzerra.com.
We will have a web-meeting walkthrough of the chembldb core schema on Friday 20th November at 3pm GMT. The excellent webhuddle will be used, so if you are interested it may be worth checking this out, setting up an account, checking it works on your machine, in advance of the meeting. Mail us if you want links to the phone number and webhuddle link.
The ChEMBL job is (W/09/087/EBI). Closing date is the 30th November 2009.
The image above is a visualisation of the continental United States of America, visualised by distance to the nearest McDonald's restaurant. Further details and attribution are in the image itself.
<NAME="Pazopanib"> <SMILES="O=S(=O)(N)c1c(ccc(c1)Nc2nccc(n2)N(c4ccc3c(nn(c3C)C)c4)C)C"> <InChI="InChI=1/C21H23N7O2S.ClH/c1-13-5-6-15(11-19(13)31(22,29)30)24-21-23-10-9-20(25-21)27(3)16-7-8-17-14(2)28(4)26-18(17)12-16;/h5-12H,1-4H3,(H2,22,29,30)(H,23,24,25);1H" > <InChIKey="MQHIQUBXFFAOMK-UHFFFAOYAU"> <ChemDraw=Pazopanib.cdx>The manufacturer of Pazopanib is GlaxoSmithKline and the product website is www.votrient.com.
Sunday, 8 November 2009
The chembldb SAR data and an initial front end is now available (see earlier posts), over the next few months we will be making quite a few changes to the data, the database, and so forth. Most excitingly, there is a large bolus of 'new' data to add. Most of the changes we make will be evolutionary, but there will be a few major things as well.
With this in mind, please mail us if you are building any systems that rely on the data, this way we can tell you in advance specifically what we are intending to do, and secondly, you could request features, cross-references, and so forth that could make your life so much easier.
I can't remember where I found the image above, but it is a little bit funny, for those of us that travel in economy/coach.