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).