Biology + chemistry -> bioinformatics + chemoinformatics

(Sorry for the gap in frequency of postings, end of quarter gets busy…)  Last week, I attended a fascinating talk by Brian Shoichet of UCSF.   He talked about much of his work in pharmaceutical science, including great work docking small molecules to proteins.  But the work that excited me the most was his efforts to look at classes of drugs (grouped together based on a common target) and predict potential cross-interactions based on chemical similarities within these classes.  The work is introduced in J Chem Inf Model. 2008 Apr;48(4):755-65. Epub 2008 Mar 13. I think this is fascinating work.   This really raises the more general issue of the meeting of biology and chemistry–clearly not a new phenomenon since “without chemistry, life itself would be impossible” (thanks, Monsanto).  However, the increased interest in using modern informatics techniques to analyze small molecules in the context of biological macromolecules is pretty exciting.    Part of this renaissance stems from the increased availability of small molecule information via PubChem and similar projects.   A critical need is open source tools for small molecule informatics processing, and I believe these are starting to emerge (not fast enough, I have a student looking hard for a basic package upon which we can build).  But this will be very exciting, because it allows us to connect the substantial literatures on manipulating chemical information (chemoinformatics) with that on manipulating biological information (bioinformatics).  I will write more on this, but it is a good topic–and one that is emerging in response to a growing impatience for molecular-level understanding of key biological processes and interactions–in response to the proliferation of associative science (e.g. X is associated with Y, but without a firm mechanistic understanding).  

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5 comments

  1. > A critical need is open source tools for small
    > molecule informatics processing, and I believe
    > these are starting to emerge

    Well the CDK and OpenBabel have been around for quite some time 🙂

  2. “A critical need is open source tools for small molecule informatics processing, and I believe these are starting to emerge (not fast enough, I have a student looking hard for a basic package upon which we can build).”

    OpenBabel, CDK, RDKit. Or all three – Cinfony.

  3. This is very interesting because it is what we are doing just know. Chemoinformatics and bioinformatics, a database of small molecules (MMsINC) and an API development for the analysis and search tools. We are 2 academic groups in Italy (Padova and Sardinia) and we are open to collaborations.

  4. Russ,
    I fell into your blog throught Google. While not open source specifically, Ariadne is just launching a commercially supported product to specifically pick out small molecule to protein, to disease, and several other biological concept entities from electronically stored text sources. It will be lauched at a product call ChemEffect and was made to meet standards required by some of the larger pharmas.

    While the backend programming is not open, the program is open designed to be modified by users and the entities level for non-programmer users and by extraction patterns at an advanced level.

    It might help! Just a thought.
    Cheers.

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