https://github.com/compomics/pepshell

Visualization of conformational proteomics data.

Science Score: 23.0%

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Low similarity (11.3%) to scientific vocabulary

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Repository

Visualization of conformational proteomics data.

Basic Info

Host: GitHub
Owner: CompOmics
License: other
Language: Java
Default Branch: master
Homepage:
Size: 2.53 MB

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Stars: 0
Watchers: 13
Forks: 0
Open Issues: 7
Releases: 0

Archived

Created almost 11 years ago · Last pushed over 3 years ago

Metadata Files

Readme License

Pepshell

Tool Description
Downloads
Usage
Project Description
Project Support

Tool Description

PepShell is a peptide centric tool that allows the visualization, analysis, and interpretation of (quantitative) conformational proteomics data. PepShell provides the user with the ability to compare the results from different experiments, and thus allows changes in protein conformation to be detected between different experimental conditions. PepShell can read data from each of the most common forms of conformational proteomics approaches, including limited proteolysis, hydrogen-deuterium exchange (HDX), and MS footprinting.

Citation

Vandermarliere et al: J Proteome Res. 2015 Apr 3;14(4):1987-90.
If you use Pepshell as part of a paper, please include the reference above.

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Downloads

Example Datasets

Test files can be found here.

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Usage

See the wiki for additional information on how to use Pepshell.

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Project Description

Proteins are dynamic molecules; they undergo crucial conformational changes induced by post-translational modifications and by binding of cofactors or other molecules. The characterization of these conformational changes and their relation to protein function is a central goal of structural biology. Unfortunately, most conventional methods to obtain structural information do not provide information on protein dynamics. Therefore, mass spectrometry-based approaches such as limited proteolysis, hydrogen-deuterium exchange and stable-isotope labeling are nowadays frequently used to characterize protein conformation and dynamics. Here, we present PepShell, a tool that allows interactive data analysis of mass spectrometry-based conformational proteomics studies by visualization of the identified peptides both at the sequence and at the structure level. Moreover, PepShell allows the comparison of experiments under different conditions including different proteolysis times or binding of the protein to different substrates or inhibitors.

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