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Title |
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HBNG: Graph theory-based visualization of hydrogen bond networks in protein structures
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Authors |
Abhishek Tiwari1*& Vivek Tiwari2 |
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Affiliation |
1GVK Biosciences, Informatics Division, Hyderabad-500037, India; 2 CIDSH, Lucknow-226020, India |
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abhishek.twr@gmail.com; * Corresponding author
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Article Type |
Hypothesis
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Date |
received April 10, 2007; revised May 28, 2007; accepted June 03, 2007; published online July 09, 2007
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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.
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Keywords
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cooperativity; anticooperativity; digraph; DOT Script; graphviz |
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| Availability |
Program is available from the authors for non-commercial purposes. |
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Citation |
Tiwari & Tiwari, Bioinformation 2(1): 28-30 (2007) |
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Edited by |
R. Sowdhamini
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ISSN |
0973-2063
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Publisher |
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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.
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