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A Fold Recognition Approach to Modeling of Structurally Variable Regions
University of Skövde, School of Humanities and Informatics.
2004 (English)Independent thesis Advanced level (degree of Master (One Year))Student thesis
Abstract [en]

A novel approach is proposed for modeling of structurally variable regions in proteins. In this approach, a prerequisite sequence-structure alignment is examined for regions where the target sequence is not covered by the structural template. These regions, extended with a number of residues from adjacent stem regions, are submitted to fold recognition. The alignments produced by fold recognition are integrated into the initial alignment to create a multiple alignment where gaps in the main structural template are covered by local structural templates. This multiple alignment is used to create a protein model by existing protein modeling techniques.

Several alternative parameters are evaluated using a set of ten proteins. One set of parameters is selected and evaluated using another set of 31 proteins. The most promising result is for loop regions not located at the C- or N-terminal of a protein, where the method produces an average RMSD 12% lower than the loop modeling provided with the program MODELLER. This improvement is shown to be statistically significant.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2004. , 50 p.
Keyword [en]
protein structure prediction; loop modeling; fold recognition; threading; structurally variable regions
National Category
Computer Science
Identifiers
URN: urn:nbn:se:his:diva-902OAI: oai:DiVA.org:his-902DiVA: diva2:3322
Presentation
(English)
Uppsok
Technology
Supervisors
Available from: 2008-02-27 Created: 2008-02-27 Last updated: 2009-11-16

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CiteExportLink to record
Permanent link

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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf