Published 2024
| Version 2
Technical note
Open
PTMVision: An Interactive Visualization Webserver for Post-Translational Modifications of Proteins
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 |
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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22.2 MB | Preview Download |
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425.3 MB | Download |
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30.6 MB | Preview Download |
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