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HBonanza specifications

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Unique identifier OMICS_14098
Name HBonanza
Alternative name Hydrogen-Bond analyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Molecular dynamics trajectories
Input format PDB
Output data Visualization script
Output format TCL
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.01
Stability Stable
Source code URL http://rocce-vm0.ucsd.edu/data/sw/hosted/hbonanza//HBonanza_1.01.py
Maintained Yes

Versioning


No version available

Publication for Hydrogen-Bond analyzer

HBonanza citation

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Identification of a pKa regulating motif stabilizing imidazole modified double stranded DNA

2014
PMCID: 4288195
PMID: 25520197
DOI: 10.1093/nar/gku1306

[…] dna duplex., the calculated trajectories were visualized using vmd 1.9.1 () while further in-depth analysis was performed using 3dna () for the structural and conformational dna parameters and the hbonanza () python script for hydrogen bond analysis. further data post-processing and analysis utilized various vmd plugins complemented with custom-made matlab scripts., persistence and quality […]


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HBonanza institution(s)
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA; Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, University of California San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California San Diego, La Jolla, CA, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
HBonanza funding source(s)
This work was carried out with funding from NIH GM31749, NSF MCB-0506593, and MCA93S013.

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