Has anyone attempted to implement the calculation of Andrew's Binding Energy (Andrews, et al., J. Med. Chem.
27 (1984) 1648) using Pipeline Pilot (only) components? If so, can you provide a copy of your code.
This so called binding energy is a rather curious item. The function for the binding energy is derived from
ligand structure and experimentally measured binding free energies for a number of small molecules against
a diverse set of targets. There are no terms involving direct interactions of the ligand with the enzyme or
receptor. Hence, it is not simply a QSAR model for a set of ligands against a particular target.
Hence, is this quantity something meaningful or useful i.e., perhaps some kind of an "intrinsic"
binding free energy (as claimed in the article) that might have utilty in drug design or is it some
kind of ad hoc fitting that has unclear, or questionable value? Hmmm...
Also, I would be interested to learn if others have attempted to develop a similar "ligand only" function
that goes beyond this 1984 publn with more ligands, more measurements, etc. How did you
construct such a function? How did you use it? Was it useful in drug design? How so?
I greatly welcome comments, ideas, suggestions, critique, etc.
Thank you.
Regards,
Jim Metz
