Abstract
Post-translational modifications (PTMs) of proteins play essential roles in governing the functions and dynamics of proteins and are implicated in many cellular processes. Several types of PTMs have been investigated through computational approaches, including phosphorylation, sumoylation, palmitoylation, and lysine and arginine methylation, among others. Because the large diversity in the user interfaces (UIs) of different prediction servers for PTMs could possibly hinder experimental biologists in using these servers, we propose to develop a protocol for a unified UI for PTM prediction servers, based on our own work and that of other groups on PTM site prediction. By following this protocol, tool developers can provide a uniform UI regardless of the PTM types and the underlying computational algorithms. With such uniformity in the UI, experimental biologists would be able to use any PTM prediction server compliant with this protocol once they had learned to use one of them. It takes a typical PTM prediction server compliant with this unified UI several minutes to calculate the prediction results for a protein 1,000 amino acids in length.
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Acknowledgements
F. Zhou's and Y. Xu's work is supported in part by the National Science Foundation (NSF/DBI-0354771, NSF/ITR-IIS-0407204, NSF/DBI-0542119, NSF/CCF0621700) and a Distinguished Scholar award from the Georgia Cancer Coalition. Y. Xue's and X. Yao's work is supported by Chinese Natural Science Foundation (39925018, 30270654 and 30270293), Chinese Academy of Science (KSCX2-2-01), Chinese 973 project (2002CB713700), Chinese Minister of Education (20020358051), American Cancer Society (RPG-99-173-01), National Institutes of Health (DK56292; CA92080) and a Distinguished Scholar award from the Georgia Cancer Coalition.
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Zhou, F., Xue, Y., Yao, X. et al. A general user interface for prediction servers of proteins' post-translational modification sites. Nat Protoc 1, 1318–1321 (2006). https://doi.org/10.1038/nprot.2006.209
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DOI: https://doi.org/10.1038/nprot.2006.209
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