by M. A. Hallen, P. Gainza, and B. R. Donald.

Duke University

11(5): 2292-2306. doi:10.1021/ct501031m

**Abstract.**
In macromolecular design, conformational energies are sensitive to small changes in atom coordinates; thus, modeling the small, continuous motions of atoms around
low-energy wells confers a substantial advantage in structural accuracy. However, modeling these motions comes at the cost of a very large number of energy
function calls, which form the bottleneck in the design calculations. In this work, we remove this bottleneck by consolidating all conformational energy
evaluations into the precomputation of a local polynomial expansion of the energy about the "ideal" conformation for each low-energy,
"rotameric" state of each
residue pair. This expansion is called "energy as polynomials in internal coordinates" (EPIC), where the internal coordinates can be side-chain dihedrals, backrub
angles, and/or any other continuous degrees of freedom of a macromolecule, and any energy function can be used without adding any asymptotic complexity to the
design. We demonstrate that EPIC efficiently represents the energy surface for both molecular-mechanics and quantum-mechanical energy functions, and apply it
specifically to protein design for modeling both side chain and backbone degrees of freedom.