Comments on: Open Combinatorial Chemistry in the Undergraduate Laboratory? http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023 A Scientist and the Web Sun, 22 Nov 2009 14:47:53 +0000 http://wordpress.org/?v=2.7.1 hourly 1 By: Cameron Neylon http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023&cpage=1#comment-165958 Cameron Neylon Tue, 08 Apr 2008 19:12:50 +0000 http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023#comment-165958 Yes, that would be a great tool to have and if it can be set up as a webservice as well that would be brilliant. To me it is important that this is not just enabling a specific project but that the tools can enable other open projects to go forward as well. Yes, that would be a great tool to have and if it can be set up as a webservice as well that would be brilliant. To me it is important that this is not just enabling a specific project but that the tools can enable other open projects to go forward as well.

]]> By: Jean-Claude Bradley http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023&cpage=1#comment-165822 Jean-Claude Bradley Tue, 08 Apr 2008 17:43:43 +0000 http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023#comment-165822 Daen - let us know when you make it available. Rajarshi Guha has set up a web service to generate Ugi products from lists of starting materials: http://rguha.ath.cx/%7Erguha/cicc/combilib/vl It would be great to have more such services available to the public Daen - let us know when you make it available. Rajarshi Guha has set up a web service to generate Ugi products from lists of starting materials:
http://rguha.ath.cx/%7Erguha/cicc/combilib/vl
It would be great to have more such services available to the public

]]> By: pm286 http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023&cpage=1#comment-165787 pm286 Tue, 08 Apr 2008 17:28:31 +0000 http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023#comment-165787 (2) Thanks, although I'd welcome clarification. Are you saying that you have modified OB to give the same functionality? If so I assume you have committed and the OB community is happy. Are you also saying that you have an Open set of attachment chemistries, deprotection strategies, etc.? Because if so, and it makes sense, I may well wish to integrate the functionality into CML (which itself does a simple sort of combinatorial molecule generation but without the additional bits you mention). (2) Thanks, although I’d welcome clarification. Are you saying that you have modified OB to give the same functionality? If so I assume you have committed and the OB community is happy. Are you also saying that you have an Open set of attachment chemistries, deprotection strategies, etc.? Because if so, and it makes sense, I may well wish to integrate the functionality into CML (which itself does a simple sort of combinatorial molecule generation but without the additional bits you mention).

]]> By: Daen de Leon http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023&cpage=1#comment-165650 Daen de Leon Tue, 08 Apr 2008 16:00:08 +0000 http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023#comment-165650 I've developed a tool on top of OpenBabel which I've called a CombChem Engine (CCE). It reads pools of compounds, deprotection strategies and attachment chemistries and produces a bunch of compounds according to those rules. The tool itself was written for a biotech client of mine, so I can't release it publicly. However, I modified some of the OB source in order to get it to work, and I will make those alterations publicly available. I’ve developed a tool on top of OpenBabel which I’ve called a CombChem Engine (CCE). It reads pools of compounds, deprotection strategies and attachment chemistries and produces a bunch of compounds according to those rules. The tool itself was written for a biotech client of mine, so I can’t release it publicly. However, I modified some of the OB source in order to get it to work, and I will make those alterations publicly available.

]]> By: Jean-Claude Bradley http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023&cpage=1#comment-162862 Jean-Claude Bradley Sun, 06 Apr 2008 12:44:02 +0000 http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1023#comment-162862 Yes for the person who runs the teaching lab this is definitely more work. That's why I was thrilled that Brent was willing to put in the time and order the chemicals. The first lab starts tomorrow: http://usefulchem.blogspot.com/2008/04/were-gonna-ugi-all-night.html In terms of purification, we're sticking to isolation by filtration of a precipitate. Those reactions that don't precipitate are discarded. That simplifies the protocol tremendously. For now, the best source to view all the pooled data for the CombiUgi project is this GoogleDoc - the Ugi Master Table: http://spreadsheets.google.com/pub?key=plwwufp30hfpUERhse9y5Kw There are links to the original lab notebook pages with all the raw data for each entry Of the various libraries that we have been using: http://usefulchem.wikispaces.com/Libraries Library 3 has the list of Ugi products that we can make in my lab immediately (71K) Library 2 has the list of Ugi products that can be make from cheap starting materials available from Sigma-Aldrich marked as next-day shippable (500K) Yes for the person who runs the teaching lab this is definitely more work.
That’s why I was thrilled that Brent was willing to put in the time and order the chemicals.
The first lab starts tomorrow:
http://usefulchem.blogspot.com/2008/04/were-gonna-ugi-all-night.html

In terms of purification, we’re sticking to isolation by filtration of a precipitate. Those reactions that don’t precipitate are discarded. That simplifies the protocol tremendously.

For now, the best source to view all the pooled data for the CombiUgi project is this GoogleDoc - the Ugi Master Table:
http://spreadsheets.google.com/pub?key=plwwufp30hfpUERhse9y5Kw

There are links to the original lab notebook pages with all the raw data for each entry

Of the various libraries that we have been using:
http://usefulchem.wikispaces.com/Libraries
Library 3 has the list of Ugi products that we can make in my lab immediately (71K)
Library 2 has the list of Ugi products that can be make from cheap starting materials available from Sigma-Aldrich marked as next-day shippable (500K)

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