HBonanza statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HBonanza
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Tool usage distribution map

This map represents all the scientific publications referring to HBonanza per scientific context
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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 citations

 (4)
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Molecular features of interaction between VEGFA and anti angiogenic drugs used in retinal diseases: a computational approach

2015
Front Pharmacol
PMCID: 4624855
PMID: 26578958
DOI: 10.3389/fphar.2015.00248

[…] mplexes (Papadopoulos et al., ). The number of contacts at protein-protein interface of complexes at 3.5 Å were determined by the g_mindist tool of GROMACS, while the number of H-bond was assessed by Hbonanza. The number of contacts resulted as follows: Ranibizumab/VEGFA, 480.7 ± 0.5; Fab-bevacizumab/VEGFA, 436.5 ± 0.4; VEGFR1d2_R2d3/VEGFA, 289.9 ± 1.8. The number of H-bonds, whose location is rep […]

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

2014
Nucleic Acids Res
PMCID: 4288195
PMID: 25520197
DOI: 10.1093/nar/gku1306

[…] each 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 of bas […]

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MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

2014
BMC Bioinformatics
PMCID: 4095001
PMID: 25077693
DOI: 10.1186/1471-2105-15-S5-S1

[…] ber of specific tools have been developed to analyze single biomolecules, for example to measure the volume of pockets in proteins (Mdpocket [] and POVME []), to analyze their hydrogen bonds network (HBonanza []) or to characterize the fine structural details of DNA molecules (MDDNA[] ) during MD simulations, there is a paucity of methods to specifically analyse MD trajectories of protein complexe […]

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The Molecular Dynamics of Trypanosoma brucei UDP Galactose 4′ Epimerase: A Drug Target for African Sleeping Sickness

2012
PMCID: 3399956
PMID: 22487100
DOI: 10.1111/j.1747-0285.2012.01392.x

[…] Frames extracted from the simulation every 50 pseconds were used for hydrogen bond analysis. The program HBonanza () was set to identify all persistent hydrogen bonds present in at least 75% of the frames. Angle and distance cutoffs of 30° and 3.5 Å were used, respectively. […]


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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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