Beyond Bioinformatics

Title

Dihedral angle and secondary structure database of short amino acid fragments

Authors

Saravanan Dayalan*, Nalaka Dilshan Gooneratne, Savitri Bevinakoppa and Heiko Schroder

Affiliation

School of Computer Science and Information Technology, RMIT University, GPO Box 2474V, Melbourne 3001, Australia

E-mail*

sdayalan@cs.rmit.edu.au; * Corresponding author

Article Type

Database

Date

received November 25, 2005; revised December 18, 2005; accepted December 23, 2005; published online January 1, 2006

Dihedral angles of amino acids are of considerable importance in protein tertiary structure prediction as they define the backbone of a protein and hence almost define the protein’s entire conformation. Most ab inito protein structure prediction methods predict the secondary structure of a protein before predicting the tertiary structure because three-dimensional fold consists of repeating units of secondary structures. Hence, both dihedral angles and secondary structures are important in tertiary structure prediction of proteins. Here we describe a database called DASSD (Dihedral Angle and Secondary Structure Database of Short Amino acid Fragments) that contains dihedral angle values and secondary structure details of short amino acid fragments of lengths 1, 3 and 5. Information stored in this database was extracted from a set of 5,227 non-redundant high resolution (less than 2-angstroms) protein structures. In total, DASSD stores details for about 733,000 fragments. This database finds application in the development of ab initio protein structure prediction methods using fragment libraries and fragment assembly techniques. It is also useful in protein secondary structure prediction.

Availability

DASSD can be accessed and downloaded from http://www.cs.rmit.edu.au/dassd/

Keywords

proteins; dihedral angles; secondary structure; tertiary structure; fragments

Citation

Dayalan et al., Bioinformation 1(3): 78-80, (2006)

Edited by

Darren R. Flower

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.