"Efficient use of semidefinite programming for selection of rotamers in protein conformations"

ABSTRACT: In this paper we study a semidefinite programming relaxation of the (NP-hard) side chain positioning problem. We show that the Slater constraint qualification (strict feasibility) fails for the SDP relaxation. We then show the advantages of using facial reduction to regularize the SDP. In fact, after applying facial reduction, we have a \emph{smaller} problem that is \emph{more stable} both in theory and in practice.

work with: Forbes Burkowski and Yuen-Lam (Vris) Cheung

pdf file

Graph partitioning and vertex separator talk

GP pdf file at SCOD14 in San Diego, at UCSD.

and GP pdf file at Univ. of Calgary