SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking

Abstract

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.

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Document Details

Document Type
Technical Report
Publication Date
Apr 01, 2007
Accession Number
ADA637517

Entities

People

  • Ioannis C. Paschalidis
  • Pirooz Vakili
  • Sandor Vajda
  • Yang Shen

Organizations

  • Boston University

Tags

Communities of Interest

  • Energy and Power Technologies

DTIC Thesaurus Topics

  • Algorithms
  • Computer Programming
  • Coordinate Systems
  • Crystal Structure
  • Electronic Mail
  • Engineering
  • Free Energy
  • Frequency
  • Manufacturing Engineering
  • Molecules
  • Optimization
  • Probability
  • Sampling
  • Semidefinite Programming
  • Statistical Samples
  • Systems Engineering
  • Three Dimensional

Readers

  • Adaptive Control and Estimation with Uncertainty in Dynamic Systems.
  • Linear Algebra