A Semi-Definite programming-based Underestimation method for global optimization in molecular docking

Author

Paschalidis, Ioannis Ch ; Shen, Yang ; Vajda, Sandor ; Vakili, Pirooz

Author_Institution

Member, IEEE, Center for Information & Systems Eng., and Dept. of Manufacturing Eng., Boston University, 15 St. Mary’s St., Brookline, MA 02446, e-mail: yannisp@bu.edu

fYear

2005

fDate

12-15 Dec. 2005

Firstpage

3675

Lastpage

3680

Abstract

The paper introduces a new global optimization method that is targeted to solve molecular docking problems, an important class of problems in computational biology. The search 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 semi-definite programming problem, hence the name Semi-Definite programming based Underestimation (SDU). The optimal underestimator is used to bias sampling in the search region. A detailed comparison of SDU with a related method of Convex Global Underestimator (CGU), a discussion of the convergence properties of SDU, and computational results of the application of SDU to a number of rigid protein-protein docking problems are provided.

Keywords

Computational biology; Global optimization; Molecular docking; Semi-definite programming; Biomedical engineering; Computational biology; Manufacturing; Optimization methods; Power engineering and energy; Proteins; Sampling methods; Search methods; Shape; Systems engineering and theory; Computational biology; Global optimization; Molecular docking; Semi-definite programming;

fLanguage

English

Publisher

ieee

Conference_Titel

Decision and Control, 2005 and 2005 European Control Conference. CDC-ECC '05. 44th IEEE Conference on

Print_ISBN

0-7803-9567-0

Type

conf

DOI

10.1109/CDC.2005.1582733

Filename

1582733