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chevron_left Hydrogen-deuterium exchange chevron_right
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Protocols

HDsite specifications

Information


Unique identifier OMICS_06889
Name HDsite
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Zhong-Yuan Kan

Publication for HDsite

HDsite citations

 (2)
library_books

Computational method allowing Hydrogen Deuterium Exchange Mass Spectrometry at single amide Resolution

2017
Sci Rep
PMCID: 5476592
PMID: 28630467
DOI: 10.1038/s41598-017-03922-3

[…] states, residue averaging of the mid-point values of HDX, and utilization of the shape of the isotopic envelope to determine the distribution of deuterium on the amides of the peptide by the software HDSite. HDSite demonstrates the feasibility of determining exchange rates at single amide resolution, but it functions optimally only with high-resolution data providing enough information to produce […]

call_split

Structural Characterization of Semen Coagulum Derived SEM1(86–107) Amyloid Fibrils That Enhance HIV 1 Infection

2014
Biochemistry
PMCID: 4039337
PMID: 24811874
DOI: 10.1021/bi500427r
call_split See protocol

[…] and fibril, and in-exchange control samples, were identified by ExMS or calculated from peaks identified during manual inspection of the data.The mass peaks identified by ExMS were used as input for HDsite,, a program that attains close to amino acid resolution by deconvoluting the shape of each isotopic peak to extract the percent HDX for each residue. The percent exchange was calculated for eac […]


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HDsite institution(s)
Johnson Research Foundation, Department of Biochemistry and Biophysics, and Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

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