Dataset Information

MeMo: a web tool for prediction of protein methylation modifications.

ABSTRACT: Protein methylation is an important and reversible post-translational modification of proteins (PTMs), which governs cellular dynamics and plasticity. Experimental identification of the methylation site is labor-intensive and often limited by the availability of reagents, such as methyl-specific antibodies and optimization of enzymatic reaction. Computational analysis may facilitate the identification of potential methylation sites with ease and provide insight for further experimentation. Here we present a novel protein methylation prediction web server named MeMo, protein methylation modification prediction, implemented in Support Vector Machines (SVMs). Our present analysis is primarily focused on methylation on lysine and arginine, two major protein methylation sites. However, our computational platform can be easily extended into the analyses of other amino acids. The accuracies for prediction of protein methylation on lysine and arginine have reached 67.1 and 86.7%, respectively. Thus, the MeMo system is a novel tool for predicting protein methylation and may prove useful in the study of protein methylation function and dynamics. The MeMo web server is available at: http://www.bioinfo.tsinghua.edu.cn/~tigerchen/memo.html.

SUBMITTER: Chen H

PROVIDER: S-EPMC1538891 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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MeMo: a web tool for prediction of protein methylation modifications.

Chen Hu H Xue Yu Y Huang Ni N Yao Xuebiao X Sun Zhirong Z

Nucleic acids research 20060701 Web Server issue

Protein methylation is an important and reversible post-translational modification of proteins (PTMs), which governs cellular dynamics and plasticity. Experimental identification of the methylation site is labor-intensive and often limited by the availability of reagents, such as methyl-specific antibodies and optimization of enzymatic reaction. Computational analysis may facilitate the identification of potential methylation sites with ease and provide insight for further experimentation. Here ...[more]

PMID: 16845004

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Project description:BackgroundMost biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community.ResultsHere we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus.ConclusionsPhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

Project description:BackgroundOne of the main issues in the automated protein function prediction (AFP) problem is the integration of multiple networked data sources. The UNIPred algorithm was thereby proposed to efficiently integrate -in a function-specific fashion- the protein networks by taking into account the imbalance that characterizes protein annotations, and to subsequently predict novel hypotheses about unannotated proteins. UNIPred is publicly available as R code, which might result of limited usage for non-expert users. Moreover, its application requires efforts in the acquisition and preparation of the networks to be integrated. Finally, the UNIPred source code does not handle the visualization of the resulting consensus network, whereas suitable views of the network topology are necessary to explore and interpret existing protein relationships.ResultsWe address the aforementioned issues by proposing UNIPred-Web, a user-friendly Web tool for the application of the UNIPred algorithm to a variety of biomolecular networks, already supplied by the system, and for the visualization and exploration of protein networks. We support different organisms and different types of networks -e.g., co-expression, shared domains and physical interaction networks. Users are supported in the different phases of the process, ranging from the selection of the networks and the protein function to be predicted, to the navigation of the integrated network. The system also supports the upload of user-defined protein networks. The vertex-centric and the highly interactive approach of UNIPred-Web allow a narrow exploration of specific proteins, and an interactive analysis of large sub-networks with only a few mouse clicks.ConclusionsUNIPred-Web offers a practical and intuitive (visual) guidance to biologists interested in gaining insights into protein biomolecular functions. UNIPred-Web provides facilities for the integration of networks, and supplies a framework for the imbalance-aware protein network integration of nine organisms, the prediction of thousands of GO protein functions, and a easy-to-use graphical interface for the visual analysis, navigation and interpretation of the integrated networks and of the functional predictions.

Dataset Information

MeMo: a web tool for prediction of protein methylation modifications.

Publications

MeMo: a web tool for prediction of protein methylation modifications.

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