Efficient use of semidefinite programming for selection of rotamers in protein conformations and other applications
Efficient use of semidefinite programming for selection of rotamers in protein conformations and other applications
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Henry Wolkowicz, University of Waterloo
In this paper we study a semidefinite programming relaxation of the (NP-hard)Ìýside chain positioning problem. We show that the Slater constraint qualificationÌý(strict feasibility) fails for the SDP relaxation. We then show the advantagesÌýof using facial reduction to regularize the SDP. In fact, after applying facialÌýreduction, we have a smaller problem that is more stable both in theory and inÌýpractice.ÌýWe include a discussion of the background of SDP relaxations and exploitingÌýpecial structure in various applications such as sensor network localization, SNL. ÌýWork with: Forbes Burkowski (University of Waterloo) Yuen-Lam CheungÌýVoronin (University of Colorado, Boulder)