Workshop on Systems Biology, Tue, 06 Nov, 2007
Speaker: Jaydeep Bardhan
Abstract
Computational molecular design represents one of the most challenging theoretical and computational problems in modern biology. The design space of possible chemicals is fantastically large and discrete, the objective function or constraints are unclear, and likely to be highly nonconvex if they were known. Furthermore, even the objective function
(binding free energy) that we do have a theoretical basis for computing can only be approximated. Exploring the design space by enumeration is out of the question, so one wishes to design. A simple model for the free energy of binding in fact, allows such a template to be determined for the electrostatic component of the binding interaction. A linear-response continuum model, under physically reasonable assumptions, gives rise to a convex, quadratic optimization
problem. This optimization theory has been widely applied, with notable successes. Computational methods are currently being developed to significantly reduce the needed time for these optimizations, and these methods will be presented as well.
URL: www.ricam.oeaw.ac.at/specsem/ssqbm/participants/abstracts/index.php
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