I find structural biology absolutely fascinating. I delight in finding and
solving computational problems that emerge from structural biology. My first
publication resulted from collaboration with Professors David and Jane Richardson
at Duke. The biological problem they were
interested in was the placement of hydrogen atoms into crystal structures (J. M.
Word, S. C. Lovell, J. S. Richardson, and D. C. Richardson (1999) "Asparagine
and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide
Orientation." JMB 285, 1735-47). They had previously used a brute force
approach to find the minimum energy placement of hydrogen atoms into a given
structure. Our improvement came in replacing the brute force approach with a
dynamic programming algorithm. With this better algorithm, we observed a
speedup of seven orders of magnitude.
Andrew Leaver-Fay, Yuanxin Liu, and Jack Snoeyink.
Faster placement of hydrogen atoms in protein structures by dynamic programming
in the Workshop on Algorithm Engineering and Experiments, 2004
(ALENEX 2004).
[PDF]
Andrew Leaver-Fay, Brian Kuhlman, and Jack Snoeyink.
An Adaptive Dynamic Programming Algorithm for The Side Chain Placement Problem
in the Pacific Symposium on Biocomputing, 2005
(PSB 2005).
[PDF]
Andrew Leaver-Fay, Brian Kuhlman, and Jack Snoeyink.
Rotamer-Pair Energy Calculations Using a Trie Data Structure
appearing in 5th Workshop on Algorithms in Bioinformatics
(WABI 2005).
Published by
Springer.
[PDF].
Copyright, Springer-Verlag
Andrew Leaver-Fay, Glenn Butterfoss, Jack Snoeyink, and Brian Kuhlman.
Maintaining solvent accessible surface area under rotamer substitution for protein design Journal of Computational Chemistry, 2007, Feb 6.
[Download]
Andrew Leaver-Fay, Yuanxin Liu, Jack Snoeyink, and Xueyi Wang.
Faster placement of hydrogen atoms in protein structures by dynamic programming
The Journal of Experimental Algorithms, 2007. Volume 12.
[Available Soon]
