Tuesday, March 28, 2006

Another angle to tackle malaria

Our malaria testing collaborator in the news:

"Our findings have the potential to be very significant on several fronts," said Lawrence W. Bergman, Ph.D., Professor of Microbiology and Immunology at Drexel University College of Medicine.

"Having determined the atomic structure of a key motor complex that is absolutely required for the parasite to enter cells, we can begin a process called structure-guided drug design," Bergman added.

From Keralanext.com

Thursday, March 23, 2006

Status of experimental work - month 2

We have now been trying for 2 months to execute on the synthetic work we planned for the diketopiperazine malaria project. There are now 4 students working on this: 2 graduate students Alicia and Khalid, and 2 undergrads James and Brett. And we might get one more undergrad next week.

Things have been progressing slowly since all of these students are new to this type of labwork. And it certainly does not help that our electrospray mass spec and NMR have both been down and will likely continue to be down for a few more months. We have a sweet new 500 MHz NMR getting set up but it will take time for it to be available. Anyone out there in the Philly area want to contribute some NMR time in the interim?

So in the meantime, we'll stick to old school TLC and common orgo sense. We ordered some TLC stains to improve the monitoring of the reactions and will keep at it.

Monday, March 20, 2006

Interview with Steve Bryant

I recently interviewed PubChem's Steve Bryant who explained the origins and inspiration behind this growing open access repository of molecular structures and information. He also provided some insights into why it is important that such resources are available to scientists for free and hinted at where the resource stands at present with regard to the CAS conflict. He also addressed the issue of errors that arose on the CHMINF-L discussion group recently. As a former protein crystallographer, he explained that it comes as no surprise that the source of the errors was simply a lack of rigorous caretaking on the part of the Protein Data Bank when it comes to small molecules and ligands.

You can read the complete interview with Steve Bryant in the March issue of Reactive Reports, which appeared today.

Tuesday, March 07, 2006

CMLRSS attempt

With some help from Egon Willighagen and Peter Murray-Rust, I have been trying to get CMLRSS to work on our molecules blog RSS feed. I was able to generate CML using OpenBabel and incorporate it in Blogger for molecule 66 but I was unable to test it because there is currently a problem the the CMLRSS readers. Egon is working on getting a reader to work in Bioclipse and will report on his progress in his blog.

Having a working CMLRSS reader is an important step in cheminformatics because it will enable the user to manipulate molecules as molecules, not just static images. For example the subscriber would be able to rotate the molecule, view it using different representation formats, measure bond lengths, etc. directly inside of the reader.

CML (Chemical Markup Language) is a kind of XML that allows for the representation of chemical information.

I interviewed a grad student yesterday who is interested in cheminformatics. He is going to start by trying to use existing web services to automatically process information (molecular weight by Rajarshi Guha for example) in our molecules blog.

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