Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction

Loading...
Thumbnail Image
File version
Author(s)
Faraggi, Eshel
Yang, Yuedong
Zhang, Shesheng
Zhou, Yaoqi
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Date
2009
Size

3593438 bytes

File type(s)

application/pdf

Location
License
Abstract

Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., threestate secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.

Journal Title

Structure

Conference Title
Book Title
Edition
Volume

17

Issue

11

Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement

© 2009 Elsevier Ltd. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher. Please refer to the journal's website for access to the definitive, published version.

Item Access Status
Note
Access the data
Related item(s)
Subject

Bioinformatics

Chemical Sciences

Biological Sciences

Information and Computing Sciences

Persistent link to this record
Citation
Collections