Determining protein structures from NOESY distance constraints by semidefinite programming.

ABSTRACT: Contemporary practical methods for protein nuclear magnetic resonance (NMR) structure determination use molecular dynamics coupled with a simulated annealing schedule. The objective of these methods is to minimize the error of deviating from the nuclear overhauser effect (NOE) distance constraints. However, the corresponding objective function is highly nonconvex and, consequently, difficult to optimize. Euclidean distance matrix (EDM) methods based on semidefinite programming (SDP) provide a natural framework for these problems. However, the high complexity of SDP solvers and the often noisy distance constraints provide major challenges to this approach. The main contribution of this article is a new SDP formulation for the EDM approach that overcomes these two difficulties. We model the

SUBMITTER: Alipanahi B 

PROVIDER: S-EPMC3619149 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature