December 2004 - chemweb - imperial.ac.uk

GMAIL invitations
by Michael Engel 21 Dec '04

21 Dec '04

Anyone interested in receiving a GMAIL invitation ? I have some spare ones. If yes, please mail me at mkengel(a)gmail.com Cheers Michael Engel -------forward------ -------- If you haven't already heard about Gmail, it's a new search-based webmail service that offers: - 1,000 megabytes (one gigabyte) of free storage - Built-in Google search that instantly finds any message you want - Automatic arrangement of messages and related replies into "conversations" - Text ads and related pages that are relevant to the content of your messages Gmail is still in an early stage of development. But If you set up an account, you'll be able to keep it even after we make Gmail more widely available. We might also ask for your comments and suggestions periodically and we appreciate your help in making Gmail even better. Thanks, The Gmail Team To learn more about Gmail before registering, visit: http://gmail.google.com/gmail/help/benefits.html (If clicking the URLs in this message does not work, copy and paste them into the address bar of your browser).

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What does the term "scholar" mean"
by Rzepa, Henry 14 Dec '04

14 Dec '04

Vis, http://pubs.acs.org/cen/news/8250/8250acs.html where apparently the use of the term "scholar" is being challenged by the ACS. I have to be careful when I talk about my scholarly activities! -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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[QSAR-devel] Molecular Open Web Services (fwd from pm286@cam.ac.uk)
by Eugen Leitl 12 Dec '04

12 Dec '04

----- Forwarded message from Peter Murray-Rust <pm286(a)cam.ac.uk> ----- From: Peter Murray-Rust <pm286(a)cam.ac.uk> Date: Sun, 12 Dec 2004 16:17:09 +0000 To: JOELib devel <joelib-devel(a)lists.sourceforge.net>, JOELib help <joelib-help(a)lists.sourceforge.net>, cdk <cdk-devel(a)lists.sourceforge.net>, Octet Developer <octet-devel(a)lists.sourceforge.net>, QSAR Development <qsar-devel(a)lists.sourceforge.net>, OpenBabel-discuss(a)lists.sourceforge.net, Beda Kosata <beda(a)zirael.org> Cc: yong Zhang <yz237(a)cam.ac.uk>, h.rzepa(a)ic.ac.uk, smt40(a)cam.ac.uk, joe Townsend <jat45(a)cam.ac.uk> Subject: [QSAR-devel] Molecular Open Web Services X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 [Crossposted to several OpenSource lists - please reply thoughtfully. I will collate significant replies] We have been investigating Web Services as a means of distributing Open molecular functionality. YY has set up a range of services on our site: http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere I believe that web services provide a valuable approach for some of what we want to do. Rather than linking a library or executable into the code, a call is made to a WS. Thus, for example, we have set up an InChI server: http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=generateinchi&JavaScript… where the input is supplied as CML or legacy ASCII and the output returned as ASCII. Note that WS do not require graphical i/o or a human to click for the service - they can be called programmatically from a wide range of bindings (probably not FORTRAN) WS have several advantages: - the user doesn't have to install the code - the user doesn't have to maintain the code - complex architectures can be hidden behind the surface - it leads to cleaner component design - the developer may not have to worry about porting - it avoids the "jar explosion and version" problem that we have when using other systems - assuming the WS is open it can be cloned and installed elsewhere, thus adding redundancy - several generic systems (e.g. http://taverna.sf.net) are being developed to support component-based approaches including WS. - attractive when the operation is a relatively infrequent requirement - good for teaching There may be some disadvantages: - the user may not always be connected or the service is not available. Solution: install the service on your local machine and/or create mirrors - there may be a performance hit - is this is actually a problem? - the application requires the state to be maintained (WS are easier for stateless protocols). All our protocols are stateless. I think WS has a lot to offer our community. For example I'd like to use JOELib or CDK to calculate molecular properties. It's an effort to link these into a single bloated app as every time some library changes the whole lot has to be recompiled. With WS I can calculate the properties I want independently of the implementation. Are others in this community interested? What services would people like? Our own list includes but is not limited to: - calculate 2D coords for connection table - calculate 3D coords for molecule - MM, MD, MO calculations - calculate descriptors for molecule - calculate properties for molecules - legacy conversions - search databases - create SVG diagrams for molecules and reactions - create PNGs If you have a working application it's relatively easy to create a WS. YY has created pages: http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage http://wwmm.ch.cam.ac.uk/moin/WebServiceDev P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Qsar-devel mailing list Qsar-devel(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/qsar-devel ----- End forwarded message ----- -- Eugen* Leitl <a href="http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net

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[QSAR-devel] Chemical Semantic Web and Thanks (fwd from pm286@cam.ac.uk)
by Eugen Leitl 08 Dec '04

08 Dec '04

----- Forwarded message from Peter Murray-Rust <pm286(a)cam.ac.uk> ----- From: Peter Murray-Rust <pm286(a)cam.ac.uk> Date: Wed, 08 Dec 2004 09:50:16 +0000 To: JOELib devel <joelib-devel(a)lists.sourceforge.net>, JOELib help <joelib-help(a)lists.sourceforge.net>, cdk <cdk-devel(a)lists.sourceforge.net>, Octet Developer <octet-devel(a)lists.sourceforge.net>, QSAR Development <qsar-devel(a)lists.sourceforge.net>, OpenBabel-discuss(a)lists.sourceforge.net, Beda Kosata <beda(a)zirael.org> Subject: [QSAR-devel] Chemical Semantic Web and Thanks X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 [Crossposted to several OpenSource lists - please reply thoughtfully. I will collate significant replies] I presented an invited lecture at the Royal Soc Chem yesterday on "The Chemical Semantic Web" and highlighted the impressive contribution of the Open Source movement in chemistry. I hope I managed to acknowledge most people's contributions. It generated a lively discussion in which, I think, the Open Source approach came out very positively. Two common negative questions were presented: "Who pays for it" the implication was that if there was no commercial development the software was second-class and there was no future for it. My response was that the code would be eagerly adopted by the bioinformatics community (strongly confirmed by Mike Ashburner) and we are starting to set up strong links with the Bioinformatics community on small molecules. This question came from the pharma industry and so I challenged them to put something back into the communal process. It's noticeable that the pharma industry is a consumer of our efforts but has not contributed anything in return and continues to pay for overpriced software products that do not use modern methodology. (I spent 15 years in Glaxo so I feel I have a right to criticise the industry). I know that pharma industry reads this list and I would be delighted if there were some who wished to support communal activity. [I would suggest they mail me directly and I will summarise replies. All replies will be assumed to be Open unless specifically indicated]. One approach would be to support a physical workshop on chemical open source. Particular topics could be: - markup languages - communal chemical ontologies (e.g. descriptors) - Open datasets - use of InChI (we are very excited about this) - graphical components - common code libraries - web services (I'll mail later) The only contribution that I know of from the pharma industry to chemoinformatics is the JME editor which is free, but despite repeated requests is not Open and not likely to be. It could be withdrawn at any time. "Open source is unfair to commercial developers" I think this attitude is particularly strong in the US and perhaps Germany. The idea is that public funding should not be used to compete against commercial organisations. As Mike Ashburner replied, most Open software in bioinformatics is written by people on short term contracts often with no possibility of extension. I know that made contributors to these lists do not have jobs. I developed much of CML when I was unemployed after being made redundant from Glaxo. I would be more (slightly) more sympathetic to this view if the chemical software industry provided anything substantial to the community. I know of no support for Open efforts from the chemical software industry other than a very undersupported effort to get an Open Management Group spec for chemistry. I was invited to contribute CML as the core of this spec, but even then it was made clear that I would not even have my (foreign) travel expenses paid - even though I had no job. Note that "free" is not good enough and may even by counterproductive. Closed software often stifles development as there is no API and the software can be withdrawn at any time. That is why we are so keen to see a JChempaint component as a universal Open chemical editor for the web. In fact I think the tide is turning. The components that you are all developing are ideal for Web Services, which will have the potential to rapidly become a major player in the chemoinformatics market. Between the members of this community we have standards, data, transformers, algorithms, repositories, query languages, graphics and much more. I'll put forward a strategy in the next mail(s). Meanwhile - when you are hacking the latest set of bugs at 0200 in the morning, take heart - it really is appreciated - and yes - the day of Open Source for "chemistry" is dawning. In fact I think the centre of gravity of chemical software development is starting to shift towards bioscience [and materials] so that people will simply refer to the informatics of small molecules as "bioinformatics" Best P. Many thanks to those who have sponsored our Open Source development: Royal Soc. Chemistry, Nature Publishing Group, Cyprotex. More about this later. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Qsar-devel mailing list Qsar-devel(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/qsar-devel ----- End forwarded message ----- -- Eugen* Leitl <a href="http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net

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Re: FW: [chemweb] ORGLIST: SMILES List of Cheap Starting Materials? (fwdfrom yadavm@scripps.edu) (fwd from darren.rhodes@GMAIL.COM)
by Eugen Leitl 06 Dec '04

06 Dec '04

----- Forwarded message from Darren Rhodes <darren.rhodes(a)GMAIL.COM> ----- From: Darren Rhodes <darren.rhodes(a)GMAIL.COM> Date: Mon, 6 Dec 2004 14:13:19 +0000 To: CHMINF-L(a)LISTSERV.INDIANA.EDU Subject: Re: FW: [chemweb] ORGLIST: SMILES List of Cheap Starting Materials? (fwdfrom yadavm(a)scripps.edu) Reply-To: Darren Rhodes <darren.rhodes(a)gmail.com> snip - header MDPI <http://www.mdpi.org/> "Molecular Diversity Preservation International (MDPI) is a nonprofit organization for deposit and exchange of molecular and biomolecular samples" is doing what you suggest. Publish your synthesis here ... <http://www.mdpi.org/molecules/index.htm> there just isn't any point in publishing in a closed access journal anymore. (Publishing in a closed access journal is like giving people some outdated cure for a terminal disease when a new effective cure is available). Also, I think that for this journal the author keeps the copyright. That means that if you were funded by a government agency (ie taxpayer); you aren't in the dubious position of giving away someone else's property. Apparently, it is possible for a spider to crawl the web; get molecular structures and convert them to smiles. (The chaps at Daylight will correct me if I'm wrong). If my understanding is correct this would open up a lot of the chemical catalogues on the web because the ones that didn't display structure and price would be overlooked and hence would loose revenue. There may be a programme ongoing by google to provide this service - I don't know - but it would certainly be useful. I'd be interested in seeing your wiki ... what would be of use would be a list of chemicals wanted. At the moment everyone has to try and second guess what to make in order to try and sell it. This is inefficient from the point of customer and supplier (the customers is offered something that they don't want and end up taking time to make what they need; the supplier has to try and sell something that doesn't have a strong market). Hope my comments are useful ... Darren. > Subject: ORGLIST: SMILES List of Cheap Starting Materials? > > Dear ORGLIST/CHEMINF readers, > > I recently found myself synthesizing a simple molecule which can be used > as a photoacid, namely, 4-formyl-6-methoxy-3-nitrophenoxyacetic acid, > accessible in two simple steps from vanillin*1. > > I am always surprised when I can make such interesting and useful > molecules so darn easily and cheaply, I am interested in a method where > I could produce an exhaustive list of all such molecules, i.e. every > small molecule that is synthetically accessible in under five steps from > the pool of cheap starting materials, using only "easy" reactions. > > I have a few questions, and wanted to subject myself to some > critisism/comment, I try to detail my idea below. > > What Are Cheap Starting Materials? > Naturally the definition of "cheap" depends on supply and demand (which > also drives discovery of new chemical knowledge); but I think a good > criteria would be anything I could buy on the gram scale for under $100. > This list would include things like vanillin, citronellal, carvone, > industrial dyes, natural amino acids, common acids/bases (sulphuric > acid, sodium hydroxide), cyclopentadiene, benzene, acetone, ethanol, > methanol etc. I think you get the idea. > > It is surprisingly difficult to construct such a list of starting > materials (in the form of a list of SMILES strings). Aldrich does not > seem to have the ability to query by price in their internal database > system (that is what they tell me at least). If anyone can think of a > better way to do this than burning me eyes out in front of Chemdraw and > an Aldrich catalog for a few weekends, please let me know. I think 1000 > compounds would be a good place to start. I'd put up a wiki/database > system linked to suppliers if anyone else would find value in such a > list. > > What Are Easy Reactions? > Sharpless et. al define the notion of "Click Chemistry"*2 as a set of > reactions which been demonstrated to posses very favorable > exergonicities in multiple contexts (among a few other qualifiers). The > basic idea is that the these reactions tend to "just work" and include > reactions like Diels-Alder, acetylene-azide dipolar cycloaddition and > epoxide formation/opening. While I wouldn't necessarily limit myself > strictly to "click" reactions, the idea is to limit the number of > reactions that will be applied to good easy ones. > > I haven't run across an elegant way to specify chemical reactions in > detail. I am collaborating with Gabriel Valiente, who has implemented a > basic reaction facility to PerlMol. He has also wondered if there is > some sort of algebra by which we can make smaller descriptions, specify > branched outcomes etc. that take advantage of the fact the most > reactions have very "natural" atom mappings, as opposed to the > completely explicit mappings we are using right now. I know that > Sertanty Inc. has something neat in the works, but given it is > commercial, I don't have too much of an idea. > > What Good Would It Be? > > The final result would be to iteratively apply our easy reactions to our > cheap starting materials (filtering conformationally implausible beasts, > at each step) to generate a list of compounds and plausible synthetic > routes to them. It'd be interesting to ask about the comparative > molecular diversity of the final list, and statistical information about > the synthetic routes. > > Again please let me know about any ideas about: > > a)How to get a large list of cheap compounds in the form of SMILES > strings. > b)A better way of specifying chemical reactions, rather than explicit > atom mapping (software etc.). > > *1 > Biochim Biophys Acta. 1987 Dec 11;905(2):409-16. > Proton concentration jumps and generation of transmembrane pH-gradients > by photolysis of 4-formyl-6-methoxy-3-nitrophenoxyacetic acid. > Janko K, Reichert J. > > *2 > Angew. Chem. Int. Ed. 2001, 40,2004--2021 > > _______________________________________________ > ORGLIST - Organic Chemistry Mailing List Website / Archive / FAQ: > http://www.orglist.net To post a message (TO EVERYBODY) send to > everybody(a)orglist.net To unsubscribe, send to > everybody-request(a)orglist.net the message: unsubscribe > your_orglist_password your_address List coordinator: Joao Aires de Sousa > (coordinator(a)orglist.net) > > ----- End forwarded message ----- > -- > Eugen* Leitl <a href="http://leitl.org">leitl</a> > ______________________________________________________________ > ICBM: 48.07078, 11.61144 http://www.leitl.org > 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE > http://moleculardevices.org http://nanomachines.net > > CHMINF-L Archives (also to join or leave CHMINF-L, etc.) > http://listserv.indiana.edu/archives/chminf-l.html > Search the CHMINF-L archives at: > http://listserv.indiana.edu/cgi-bin/wa?S1=chminf-l > Sponsors of CHMINF-L: > http://www.indiana.edu/~cheminfo/chminf-l_support.html > > > _______________________________________________ > chemweb mailing list > chemweb(a)imperial.ac.uk > http://mailman.ic.ac.uk/mailman/listinfo/chemweb > List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk) > > -- If necessary use pgp key http://makeashorterlink.com/?N19042659 CHMINF-L Archives (also to join or leave CHMINF-L, etc.) http://listserv.indiana.edu/archives/chminf-l.html Search the CHMINF-L archives at: http://listserv.indiana.edu/cgi-bin/wa?S1=chminf-l Sponsors of CHMINF-L: http://www.indiana.edu/~cheminfo/chminf-l_support.html ----- End forwarded message ----- -- Eugen* Leitl <a href="http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net

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ORGLIST: SMILES List of Cheap Starting Materials? (fwd from yadavm@scripps.edu)
by Eugen Leitl 06 Dec '04

06 Dec '04

----- Forwarded message from Maneesh Yadav <yadavm(a)scripps.edu> ----- From: "Maneesh Yadav" <yadavm(a)scripps.edu> Date: Sat, 4 Dec 2004 20:48:39 -0800 To: <everybody(a)orglist.net> Subject: ORGLIST: SMILES List of Cheap Starting Materials? Dear ORGLIST/CHEMINF readers, I recently found myself synthesizing a simple molecule which can be used as a photoacid, namely, 4-formyl-6-methoxy-3-nitrophenoxyacetic acid, accessible in two simple steps from vanillin*1. I am always surprised when I can make such interesting and useful molecules so darn easily and cheaply, I am interested in a method where I could produce an exhaustive list of all such molecules, i.e. every small molecule that is synthetically accessible in under five steps from the pool of cheap starting materials, using only easy reactions. I have a few questions, and wanted to subject myself to some critisism/comment, I try to detail my idea below. What Are Cheap Starting Materials? Naturally the definition of cheap depends on supply and demand (which also drives discovery of new chemical knowledge); but I think a good criteria would be anything I could buy on the gram scale for under $100. This list would include things like vanillin, citronellal, carvone, industrial dyes, natural amino acids, common acids/bases (sulphuric acid, sodium hydroxide), cyclopentadiene, benzene, acetone, ethanol, methanol etc. I think you get the idea. It is surprisingly difficult to construct such a list of starting materials (in the form of a list of SMILES strings). Aldrich does not seem to have the ability to query by price in their internal database system (that is what they tell me at least). If anyone can think of a better way to do this than burning me eyes out in front of Chemdraw and an Aldrich catalog for a few weekends, please let me know. I think 1000 compounds would be a good place to start. Id put up a wiki/database system linked to suppliers if anyone else would find value in such a list. What Are Easy Reactions? Sharpless et. al define the notion of Click Chemistry*2 as a set of reactions which been demonstrated to posses very favorable exergonicities in multiple contexts (among a few other qualifiers). The basic idea is that the these reactions tend to just work and include reactions like Diels-Alder, acetylene-azide dipolar cycloaddition and epoxide formation/opening. While I wouldnt necessarily limit myself strictly to click reactions, the idea is to limit the number of reactions that will be applied to good easy ones. I havent run across an elegant way to specify chemical reactions in detail. I am collaborating with Gabriel Valiente, who has implemented a basic reaction facility to PerlMol. He has also wondered if there is some sort of algebra by which we can make smaller descriptions, specify branched outcomes etc. that take advantage of the fact the most reactions have very natural atom mappings, as opposed to the completely explicit mappings we are using right now. I know that Sertanty Inc. has something neat in the works, but given it is commercial, I dont have too much of an idea. What Good Would It Be? The final result would be to iteratively apply our easy reactions to our cheap starting materials (filtering conformationally implausible beasts, at each step) to generate a list of compounds and plausible synthetic routes to them. Itd be interesting to ask about the comparative molecular diversity of the final list, and statistical information about the synthetic routes. Again please let me know about any ideas about: a)How to get a large list of cheap compounds in the form of SMILES strings. b)A better way of specifying chemical reactions, rather than explicit atom mapping (software etc.). *1 Biochim Biophys Acta. 1987 Dec 11;905(2):409-16. Proton concentration jumps and generation of transmembrane pH-gradients by photolysis of 4-formyl-6-methoxy-3-nitrophenoxyacetic acid. Janko K, Reichert J. *2 Angew. Chem. Int. Ed. 2001, 40,2004--2021 _______________________________________________ ORGLIST - Organic Chemistry Mailing List Website / Archive / FAQ: http://www.orglist.net To post a message (TO EVERYBODY) send to everybody(a)orglist.net To unsubscribe, send to everybody-request(a)orglist.net the message: unsubscribe your_orglist_password your_address List coordinator: Joao Aires de Sousa (coordinator(a)orglist.net) ----- End forwarded message ----- -- Eugen* Leitl <a href="http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net

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TimBL on 10 Years of the W3C
by Rzepa, Henry 02 Dec '04

02 Dec '04

See http://news.bbc.co.uk/ => Watch BBC News in video => Select Index Sci-TEch => Experts discuss Web's future. Of course, the actual link seems to be generated by Javascript, and hence is not bookmarkable (ie apparently http://news.bbc.co.uk/nolavconsole/ukfs_news/hi/newsid_4060000/newsid_40605… ) but as this, is non functional). There are small hints of the usefulness of the Web to Life sciences, and of course of the importance of the Semantic Web. And can I sum up 10 years of the "Chemical Web" with this peer into the future: http://ipoddernet.sourceforge.net/ where one cultural phenomenon of the times is married to another (RSS) in having audio downloads to your iPod. There is a fair bit of analogy between a music track and "a molecule". PS A 1-day conference touching on many such chemical themes will be held at Cambridge on December 7th 2004. A special issue of the RSC journal OBC (issue 22) has a number of articles on this, including this one http://www.rsc.org/suppdata/OB/b4/b410732b/original/ PS This is NOT the published article (which is only available to those with an RSC subscription) but the SUPPLEMENTAL INFORMATION). -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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