An important aspect of biological macromolecules is how they interact with each other. Modeling the interaction between molecules is of great practical importance: understanding these interactions is a key element in the new field of computer-aided drug design. Unfortunately, detailed analysis of molecular interactions is computationally expensive.

When modeling the interaction between two molecules,
we can improve computational efficiency by concentrating our initial efforts
at understanding the interactions between the molecular **surfaces**,
and evaluating the detailed atomic interactions later.

This strategy has advantages for simplifying the calculations
and lowering the hardware requirements for displaying the results.
`HARMONY` computes a simplified representation of protein surfaces
using expansions of spherical harmonic functions.
These representations are useful because it gives the user
control of the resolution of the surface geometry and surface properties,
and is especially important when developing efficient
algorithms for computing and analyzing protein-protein and
protein-ligand interactions.
For example, the protein-protein docking program `SurfDock` uses
low-resolution models
for initially placing the molecules and high-resolution models for refinement
of the complex.
Details of the mathematical methods used by `HARMONY` can be found in
Duncan, B. S. and Olson, A. J. Approximation and characterization of
molecular surfaces. *Biopolymers* **33**, 219-229, 1993.

This document - still in development -
gives an introduction to `HARMONY`.
The images were rendered using
`AVS`, a data-flow visualization system,
and `AVStool`, a programmable interface to `AVS`.

Tue Feb 21 15:12:21 PST 1995