Lydia Kavraki Stanford University
Geometry and the Discovery of New Ligands
Computer-aided drug design is a significant component of
the rational approach to pharmaceutical drug design.
Chemists now consider
the geometric and chemical characteristics of molecules
early in the design process in an effort to quickly
identify ligands
that have good chances of becoming potent pharmaceutical
drugs. Computer assistance is not only helpful but
also necessary to narrow down the search for
potential ligands. Depending on the
level of accuracy desired to model
drug action, detailed quantum mechanical methods or
approximate molecular mechanics methods are used.
Even when simple approximations are made, efficient
approaches are needed to compute, among other
things, molecular surfaces and molecular volume,
models of
receptor active sites, reasonable dockings of ligands
inside protein cavities, and geometric invariants
among different ligands that exhibit similar activity.
This paper surveys several
problems and approaches in the area of computer-aided
pharmaceutical drug design and draws analogies
with problems from robotics and computational geometry.