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Title

 

 

 

 

HBNG: Graph theory-based visualization of hydrogen bond networks in protein structures

 

Authors

Abhishek Tiwari1*& Vivek Tiwari2

Affiliation

 1GVK Biosciences, Informatics Division, Hyderabad-500037, India; 2 CIDSH, Lucknow-226020, India

Email

abhishek.twr@gmail.com; * Corresponding author

 

Article Type

Hypothesis

 

Date

received April 10, 2007; revised May 28, 2007; accepted June 03, 2007; published online July 09, 2007

 

Abstract

HBNG is a graph theory-based tool for visualization of Hydrogen Bond Network in 2D. Digraphs generated by HBNG facilitate visualization of cooperativity and anticooperativity chains & rings in Protein Structures. HBNG takes Hydrogen Bonds list files (Output from HBAT, HBexplore, HBPLUS and STRIDE) as input and generates a DOT language script and constructs digraphs using freeware AT&T Graphviz tool. HBNG is useful in the enumeration of favorable topologies of hydrogen bond networks in protein structures and determining the effect of cooperativity and anticooperativity on protein stability and folding. HBNG can be applied to protein structure comparison and in the identification of secondary structural regions in protein structures.

 

Keywords

 

cooperativity; anticooperativity; digraph; DOT Script; graphviz

Availability

Program is available from the authors for non-commercial purposes.

Citation

Tiwari & Tiwari, Bioinformation 2(1): 28-30 (2007)

Edited by

R. Sowdhamini

 

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.