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

Abstract

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:
Research Org.:
Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
918349
Report Number(s):
SAND2003-8516
TRN: US200818%%357
DOE Contract Number:  
AC04-94AL85000
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; OPTIMIZATION; PROTEIN STRUCTURE

Citation Formats

Young, Malin M, Sale, Kenneth L, Gray, Genetha Anne, and Kolda, Tamara Gibson. Optimizing an emperical scoring function for transmembrane protein structure determination.. United States: N. p., 2003. Web. doi:10.2172/918349.
Young, Malin M, Sale, Kenneth L, Gray, Genetha Anne, & Kolda, Tamara Gibson. Optimizing an emperical scoring function for transmembrane protein structure determination.. United States. https://doi.org/10.2172/918349
Young, Malin M, Sale, Kenneth L, Gray, Genetha Anne, and Kolda, Tamara Gibson. 2003. "Optimizing an emperical scoring function for transmembrane protein structure determination.". United States. https://doi.org/10.2172/918349. https://www.osti.gov/servlets/purl/918349.
@article{osti_918349,
title = {Optimizing an emperical scoring function for transmembrane protein structure determination.},
author = {Young, Malin M and Sale, Kenneth L and Gray, Genetha Anne and Kolda, Tamara Gibson},
abstractNote = {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.},
doi = {10.2172/918349},
url = {https://www.osti.gov/biblio/918349}, journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Oct 01 00:00:00 EDT 2003},
month = {Wed Oct 01 00:00:00 EDT 2003}
}