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Volume 7


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In Silico Biology 7, 0057 (2007); ©2007, Bioinformation Systems e.V.  



HBAT: A complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures

Abhishek Tiwari and Sunil K. Panigrahi*

School of Chemistry, University of Hyderabad, Hyderabad 500 046, India

* Corresponding author
   Email: panigrahisk@yahoo.com


Edited by E. Wingender; received May 04, 2007; revised August 26, 2007; accepted November 11, 2007; published December 06, 2007


Abstract

The program HBAT is a tool to automate the analysis of potential hydrogen bonds and similar type of weak interactions like halogen bonds and non-canonical interactions in macromolecular structures, available in Brookhaven Protein Database (PDB) file format. HBAT is written using PERL and TK languages. The program generates an MSOFFICE Excel compatible output file for statistical analysis. HBAT identify potential interactions based on geometrical criteria. A series of analysis reports like frequency tables, geometry distribution tables, furcations list are generated. A user friendly GUI offers freedom to select several parameters and options. Graphviz based visualization of hydrogen bond networks in 2D helps to study the cooperativity and anticooperativity geometry in hydrogen bond. HBAT supports post docking interaction analysis between PDB files for any target/receptor (in PDB files) and docked ligands/poses (in SDF). This tool can be implemented in active site interaction analysis, structure based drug design and molecular dynamics simulations.


Keywords: hydrogen bond, software, geometrical analysis, water, cooperativity