Protocol abstract
Nature Protocols 1, - 1318 - 1321 (2006)
Published online: 26 October 2006 | doi:10.1038/nprot.2006.209
Subject Category: Computational and theoretical biology
A general user interface for prediction servers of proteins' post-translational modification sites
Fengfeng Zhou1,4, Yu Xue2,4, Xuebiao Yao2,3 & Ying Xu1
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.
- Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA.
- Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of China, Hefei, China 230027.
- Department of Physiology and Cancer Research Program, Morehouse School of Medicine, Atlanta, Georgia 30310, USA.
- These authors contributed equally to this work.
Correspondence to: Ying Xu1 e-mail: xyn@bmb.uga.edu
Correspondence to: Xuebiao Yao2,3 e-mail: yaoxb@ustc.edu.cn
