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Showing posts from April, 2009

New Staff In The Group

We are coming to the end of our current round of recruitment, and now have new starters regularly starting, laying claim to their part of the caravan, etc. . Here is a link to the group members.

Bioactive Peptides

Peptides (short polymers built from amide-linked alpha-amino acids) are one of the largest classes of bioactive compounds. Many drugs are peptides, or peptide derivatives; furthermore the ready accessibility of amino-acid monomers and chemistry for reliable assembly have led to very extensive characterisation of peptides as bioactives. An additional very useful property of peptide derivatives is that due to their modular nature, and the conformational constraints enforced by stereochemistry and the peptide backbone geometry, it is often possible to get some pretty good QSARs derived from amino-acid sidechain properties. It is also possible to automatically classify peptides into various subclasses (natural, non-natural, N-capped, C-capped, cyclic, etc, ) in some sort of ontology-based classification. The following is a brief overview of the peptide content of StARlite (release 31). In total, 41,128 compounds contain the simplest possible dipeptide substructure (di-glycine), this corr

Books and Papers - 10 - A Travel Guide To Scientific Sites Of The British Isles

Oh my goodness! My head is splitting - I acquired a headcold on Friday, and today am still laid low. Other than interviews tomorrow, I am sorely tempted to spend the following day with Mr. Duvet and Mrs. Pillow..... Anyway, a book, if the preface is not a call to arms, I don't know what is, this really is an essential book for every scientist (who lives in or visits the British Isles). It is also a book that when I reach for it from the shelves, the kids run to tidy up, or state they have homework. regardless, I will quote from the first couple of sentences from the preface.... The Population of the British Isles is less than 0.2% that of the entire earth ( sic ); yet this tiny fraction of human society is responsible for an enormous number of cultural advances in both the arts and sciences. Public appreciation for the men and women of Britain and Ireland who wrote, painted, composed music, etc. is evident wherever one looks, but the recognition of explorers of nature are harde

StARlite Schema Walkthrough

So, here is another StARlite schema walkthrough (barring any unforeseen circumstances). Wednesday 8th April, 2009 at 2pm UK local time, which is now BST. It will take an hour. Please mail me , if you are interested in getting the weblink. You will need to call a UK telephone, so please bear this in mind. The image is of the Starlite rooms cocktail bar in Tujunga Village, Los Angeles. I have not visited there (yet), but given Tujunga's Utopian Socialist roots, it seems a mighty fine bar to have a drink in.

Paper of the year?

Two simple words Robot Scientist . %T The Automation of Science %A Ross D. King %A Jem Rowland %A Stephen G. Oliver %A Michael Young %A Wayne Aubrey %A Emma Byrne %A Maria Liakata %A Magdalena Markham %A Pinar Pir %A Larisa N. Soldatova %A Andrew Sparkes %A Kenneth E. Whelan %A Amanda Clare %J Science %D 2009 %V 324 %P 85-89

Bioisostere Discovery

Here is an old, old use case we developed for StARlite, this one looks at using data contained within StARlite to discover bioisosteres - a functional group replacement that preserves activity while improving other properties, such as metabolism, patentability, solubility etc. The algorithm exploits the useful 'data structure' of StARlite, in that compounds are typically entered in the literature/database as clusters of synthetically related compounds ( i.e. they typically share late stage intermediates in their production), and therefore there are often reasonably straightforward ways to synthetically access these related compounds. Secondly, again because of the structure of the data, there are often equivalent assays to compare (same assays, done under the same conditions, by the same people), and so this removes one important variable from any further analysis (this is performed using the simple heuristic of only comparing quantitative data from the same StARlite doc_id