Published 2024 | Version 2
Technical note Open

PTMVision: An Interactive Visualization Webserver for Post-Translational Modifications of Proteins

  • 1. ROR icon VIB-UGent Center for Medical Biotechnology
  • 2. ROR icon Ghent University
  • 3. ROR icon University of Tübingen

Description

Source code and example application files for PTMVision:

File Description
ptmvision-code.zip The source code of PTMVision as of Nov 19, 2024.
ptmvision-image.tar.gz The Docker image of PTMVision as of Nov 19, 2024.
ptmvision-supplementary-table-1.xlsx

Description of RAW input files origin and processing procedure/methods for the use cases, i.e., the example applications in
the PTMVision manuscript and available on the web server.

ptmvision-usecases.zip

The sequences (in FASTA format), search engine outputs, and PTMVision session files for the two example applications described in detail in the PTMVision manuscript. The raw input files are not included.

ptmvision-examples.zip The input and PTMVision session files for the example sessions available on the web server. The raw input files are not included.

 

Files

ptmvision-code.zip

Files (501.7 MB)

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Additional details

Funding

Deutsche Forschungsgemeinschaft
Cellular Mechanisms of Antibiotic Action and Production TRR261
Deutsche Forschungsgemeinschaft
Cluster of 16 Excellence EXC 2124 ‘Controlling Microbes to Fight Infections 390838134
Deutsche Forschungsgemeinschaft
Cluster of Excellence EXC 2064/1 ‘Machine Learning: New Perspectives for Science 390727645
Research Foundation - Flanders
G010023N, G028821
European Commission
Horizon Europe Programme 101080544
Ghent University
Concerted Research Actio BOF21/GOA/033

Dates

Updated
2024-11-19

Software

Repository URL
https://github.com/Integrative-Transcriptomics/PTMVision
Programming language
Python, JavaScript, HTML, CSS
Development Status
Active

References

  • Ressa, A.; Bosdriesz, E.; De Ligt, J.; Mainardi, S.; Maddalo, G.; Prahallad, A.; Jager, M.; De La Fonteijne, L.; Fitzpatrick, M.; Groten, S.; others, A system-wide approach to monitor responses to synergistic BRAF and EGFR inhibition in colorectal cancer cells. Molecular & Cellular Proteomics 2018, 17, 1892–1908.
  • Schmidt, A.; Kochanowski, K.; Vedelaar, S.; Ahrné, E.; Volkmer, B.; Callipo, L.; Knoops, K.; Bauer, M.; Aebersold, R.; Heinemann, M. The quantitative and condition-dependent Escherichia coli proteome. Nature biotechnology 2016, 34, 104–110.
  • Sadecki, P. W.; Balboa, S. J.; Lopez, L. R.; Kedziora, K. M.; Arthur, J. C.; Hicks, L. M. Evolution of polymyxin resistance regulates colibactin production in Escherichia coli. ACS chemical biology 2021, 16, 1243–1254
  • audel, M.; Burkhart, J. M.; Breiter, D.; Zahedi, R. P.; Sickmann, A.; Martens, L. A complex standard for protein identification, designed by evolution. Journal of proteome research 2012, 11, 5065–5071.
  • Barbosa, A. C.; Pfister, K. E.; Chiba, T.; Bons, J.; Rose, J. P.; Burton, J. B.; King, C. D.; O'Broin, A.; Young, V.; Zhang, B.; others Dicarboxylic acid dietary supplementation protects against acute kidney injury. Journal of the American Society of Nephrology 2024, 10–1681.
  • Pfister, K.; Young, V.; Frankel, B.; Silva Barbosa, A.; Burton, J.; Bons, J.; Zhang, B.; Chiba, T.; Uhlean, R.; Goetzman, E.; others Succinylation of Park 7 Activates a Protective Metabolic Response to Acute Kidney Injury. American Journal of Physiology-Renal Physiology 2024