Title

Authors

Affiliation

Department of Computer Science, V.T.Bhattathiripad College, University of Calicut, Thenhipalam, Kerala 673635 India

Email

saritha16.namboodiri@gmail.com; *Corresponding author

Article Type

Software

Date

Received May 15, 2013; Accepted May 17, 2013; Published June 08, 2013

SpecP is an open-source Python module that performs Spectral Partitioning on Protein Contact Graphs. Protein Contact Graphs are graph theory based representation of the protein structure, where each amino acid forms a ‘vertex’ and spatial contact of any two amino acids is an ‘edge’ between them. Spectral partitioning is carried out in SpecP based on the second smallest spectral value (eigen value) of the Protein Contact Graph. The eigen vector corresponding to the second smallest spectral value are partitioned into two clusters based on the sign of the corresponding vector entry. Spectral Partitioning algorithm is repeatedly carried out until the desired numbers of partitions are obtained. SpecP visualizes the spectrally partitioned clusters of protein structure along with the Protein Contact Map and Protein Contact Graph which can be saved for later use. It also possesses an interactive mode whereby the user has the ability to zoom, pan, resize and save these raster images in various image formats (.eps, .jpg, .png) manually. SpecP is a stand-alone extensible tool useful for structural analysis of proteins.

Citation

Namboodiri & Kripadas, Bioinformation 9(10):545-548 (2013)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.