SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model
File version
Author(s)
Liu, Song
Zhou, Yaoqi
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Date
Size
115149 bytes
File type(s)
application/pdf
Location
Abstract
How to recognize the structural fold of a protein is one of the challenges in protein structure prediction. We have developed a series of single (non-consensus) methods (SPARKS, SP2, SP3, SP4) that are based on weighted matching of two to four sequence and structure-based profiles. There is a robust improvement of the accuracy and sensitivity of fold recognition as the number of matching profiles increases. Here, we introduce a new profile-profile comparison term based on real-value dihedral torsion angles. Together with updated real-value solvent accessibility profile and a new variable gap-penalty model based on fractional power of insertion/deletion profiles, the new method (SP5) leads to a robust improvement over previous SP method. There is a 2% absolute increase (5% relative improvement) in alignment accuracy over SP4 based on two independent benchmarks. Moreover, SP5 makes 7% absolute increase (22% relative improvement) in success rate of recognizing correct structural folds, and 32% relative improvement in model accuracy of models within the same fold in Lindahl benchmark. In addition, modeling accuracy of top-1 ranked models is improved by 12% over SP4 for the difficult targets in CASP 7 test set. These results highlight the importance of harnessing predicted structural properties in challenging remote-homolog recognition.
Journal Title
PL o S One
Conference Title
Book Title
Edition
Volume
3
Issue
6
Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement
© 2013 Zhang et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License CCAL. (http://www.plos.org/journals/license.html)
Item Access Status
Note
Access the data
Related item(s)
Subject
Bioinformatics