SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.
This paper introduces a new stochastic global optimization method targeting protein-protein docking problems, an important class of problems in computational structural biology. The method is based on finding general convex quadratic underestimators to the binding energy function that is funnel-like. Finding the optimum underestimator requires solving a semidefinite programming problem, hence the name semidefinite programming-based underestimation (SDU). The underestimator is used to bias sampling in the search region. It is established that under appropriate conditions SDU locates the global energy minimum with probability approaching one as the sample size grows. A detailed comparison of SDU with a related method of convex global underestimator (CGU), and computational results for protein-protein docking problems are provided.
Paschalidis
Ioannis Ch
IC
Center for Information and Systems Engineering, and Department of Manufacturing Engineering, and the Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215 USA (e-mail:  yannisp@bu.edu ).
Shen
Yang
Y
Vakili
Pirooz
P
Vajda
Sandor
S