test Browse by Author Names Browse by Titles of Works Browse by Subjects of Works Browse by Issue Dates of Works
       

Advanced Search
Home   
 
Browse   
Communities
& Collections
  
Issue Date   
Author   
Title   
Subject   
 
Sign on to:   
Receive email
updates
  
My Account
authorized users
  
Edit Profile   
 
Help   
About T-Space   

T-Space at The University of Toronto Libraries >
School of Graduate Studies - Theses >
Master >

Please use this identifier to cite or link to this item: http://hdl.handle.net/1807/24653

Title: High Throughput Prediction of Critical Protein Regions Using Correlated Mutation Analysis
Authors: Xu, Yongbai
Advisor: Tillier, Elisabeth
Department: Medical Biophysics
Keywords: Correlated Mutation Analysis
Covariation
Coevolve
Contact Prediction
Dependency
PatchD
Issue Date: 29-Jul-2010
Abstract: Correlated mutation analysis is an effective approach for predicting functional and structural residue interactions from protein multiple sequence alignments. A prediction pipeline over the Pfam database was developed to predict residue contacts within protein domains. Cross- reference with the PDB showed these contacts are spatially close. Furthermore, we found our predictions to be biochemically reasonable and correspond closely with known contact matrices. This large-scale search for coevolving regions within protein domains revealed that if two sites in an alignment covary, then neighboring sites in the alignment would also typically covary, resulting in clusters of covarying residues. The program PatchD was developed to measure the covariation between disconnected sequence clusters to reveal patch covariation. Patches that exhibited strong covariation identified multiple residues that were generally nearby in the protein structures, suggesting that the detection of covarying patches can be used in addition to traditional CMA approaches to reveal functional interaction partners.
URI: http://hdl.handle.net/1807/24653
Appears in Collections:Master
Department of Medical Biophysics - Master theses

Files in This Item:

File Description SizeFormat
Xu_Yongbai_20106_MSc_thesis.pdf11.82 MBAdobe PDF
View/Open

This item is licensed under a Creative Commons License
Creative Commons

Items in T-Space are protected by copyright, with all rights reserved, unless otherwise indicated.

uoft