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Title: Optimizing an emperical scoring function for transmembrane protein structure determination.

Optimizing an emperical scoring function for transmembrane protein structure determination. We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.
Authors: ; ; ;
Publication Date:
OSTI Identifier:OSTI ID: 918349
Report Number(s):SAND2003-8516
TRN: US200818%%357
DOE Contract Number:AC04-94AL85000
Resource Type:Technical Report
Research Org:Sandia National Laboratories
Sponsoring Org:USDOE
Country of Publication:United States
Language:English
Subject: 59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; OPTIMIZATION; PROTEIN STRUCTURE