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Experiment planning for protein stru...

Dartmouth College., Computer Science.

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Experiment planning for protein structure elucidation and site-directed protein recombination.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Experiment planning for protein structure elucidation and site-directed protein recombination./
Author:	Ye, Xiaoduan.
Description:	200 p.
Notes:	Adviser: Chris Bailey-Kellogg.
Contained By:	Dissertation Abstracts International69-10B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3330657
ISBN:	9780549855231

Experiment planning for protein structure elucidation and site-directed protein recombination.
Ye, Xiaoduan.

Experiment planning for protein structure elucidation and site-directed protein recombination. - 200 p.

Adviser: Chris Bailey-Kellogg.

Thesis (Ph.D.)--Dartmouth College, 2007.

In order to most effectively investigate protein structure and improve protein function, it is necessary to carefully plan appropriate experiments. The combinatorial number of possible experiment plans demands effective criteria and efficient algorithms to choose the one that is in some sense optimal. This thesis addresses experiment planning challenges in two significant applications. The first part of this thesis develops an integrated computational-experimental approach for rapid discrimination of predicted protein structure models by quantifying their consistency with relatively cheap and easy experiments (cross-linking and site-directed mutagenesis followed by stability measurement). In order to obtain the most information from noisy and sparse experimental data, rigorous Bayesian frameworks have been developed to analyze the information content. Efficient algorithms have been developed to choose the most informative, least expensive, and most robust experiments. The effectiveness of this approach has been demonstrated using existing experimental data as well as simulations, and it has been applied to discriminate predicted structure models of the pTfa chaperone protein from bacteriophage lambda.

ISBN: 9780549855231Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Experiment planning for protein structure elucidation and site-directed protein recombination.
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020 $a 9780549855231
035 $a (UMI)AAI3330657
035 $a AAI3330657
040 $a UMI $c UMI
100 1 $a Ye, Xiaoduan. $3 1019189
245 1 0 $a Experiment planning for protein structure elucidation and site-directed protein recombination.
300 $a 200 p.
500 $a Adviser: Chris Bailey-Kellogg.
500 $a Source: Dissertation Abstracts International, Volume: 69-10, Section: B, page: 6239.
502 $a Thesis (Ph.D.)--Dartmouth College, 2007.
520 $a In order to most effectively investigate protein structure and improve protein function, it is necessary to carefully plan appropriate experiments. The combinatorial number of possible experiment plans demands effective criteria and efficient algorithms to choose the one that is in some sense optimal. This thesis addresses experiment planning challenges in two significant applications. The first part of this thesis develops an integrated computational-experimental approach for rapid discrimination of predicted protein structure models by quantifying their consistency with relatively cheap and easy experiments (cross-linking and site-directed mutagenesis followed by stability measurement). In order to obtain the most information from noisy and sparse experimental data, rigorous Bayesian frameworks have been developed to analyze the information content. Efficient algorithms have been developed to choose the most informative, least expensive, and most robust experiments. The effectiveness of this approach has been demonstrated using existing experimental data as well as simulations, and it has been applied to discriminate predicted structure models of the pTfa chaperone protein from bacteriophage lambda.
520 $a The second part of this thesis seeks to choose optimal breakpoint locations for protein engineering by site-directed recombination. In order to increase the possibility of obtaining folded and functional hybrids in protein recombination, it is necessary to retain the evolutionary relationships among amino acids that determine protein stability and functionality. A probabilistic hypergraph model has been developed to model these relationships, with edge weights representing their statistical significance derived from database and a protein family. The effectiveness of this model has been validated by showing its ability to distinguish functional hybrids from non-functional ones in existing experimental data. It has been proved to be NP-hard in general to choose the optimal breakpoint locations for recombination that minimize the total perturbation to these relationships, but exact and approximate algorithms have been developed for a number of important cases.
590 $a School code: 0059.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Computer Science. $3 626642
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690 $a 0984
710 2 $a Dartmouth College. $b Computer Science. $3 1019183
773 0 $t Dissertation Abstracts International $g 69-10B.
790 $a 0059
790 1 0 $a Bailey-Kellogg, Chris, $e advisor
790 1 0 $a Donald, Bruce R. $e committee member
790 1 0 $a Friedman, Alan M. $e committee member
790 1 0 $a Winkler, Peter $e committee member
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3330657