Treffer: Rotamer-Pair Energy Calculations Using a Trie Data Structure.

Protein design software places amino acid side chains by precomputing rotamer-pair energies and optimizing rotamer placement. If the software optimizes by rapid stochastic techniques, then the precomputation phase dominates run time. We present a new algorithm for rapid rotamer-pair energy computation that uses a trie data structure. The trie structure avoids redundant energy computations, and lends itself to time-saving pruning techniques based on a simple geometric criteria. With our new algorithm, we compute rotamer-pair energies nearly 4 times faster than the previous approach. [ABSTRACT FROM AUTHOR]