A Peaceman-Rachford Splitting Method for the Protein Side-Chain Positioning Problem
Forbes Burkowski, Jiyoung Im, Henry Wolkowicz
TL;DR
This paper introduces a novel Peaceman-Rachford splitting method to solve a semidefinite relaxation of the NP-hard protein side-chain positioning problem, achieving near-optimal solutions efficiently.
Contribution
It develops a new splitting algorithm tailored for the DNN relaxation of SCP, improving solution accuracy and computational performance.
Findings
Almost all instances solved to optimality
Effective handling of NP-hard problem
Demonstrated efficiency of the splitting method
Abstract
We formulate a doubly nonnegative (DNN) relaxation of the protein side-chain positioning (SCP) problem. We inherit the natural splitting of variables that stems from the facial reduction technique in the semidefinite relaxation. We solve the relaxation using a variant of the Peaceman-Rachford splitting method. Our numerical experiments show that we solve almost all instances of the NP-hard SCP problem to optimality.
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
Taxonomy
TopicsDendrimers and Hyperbranched Polymers · Antiplatelet Therapy and Cardiovascular Diseases · Parkinson's Disease Mechanisms and Treatments