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Updated: Aug 9, 2026
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A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
Published on: April 29, 2022
An online literature mining tool for protein phosphorylation
1Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center Washington, DC 20007, USA.
Bioinformatics (Oxford, England)
|April 29, 2006
Summary
A new web tool, RLIMS-P, mines protein phosphorylation data from scientific literature. It extracts key information like protein kinases and phosphorylation sites, aiding biological research and database annotation.
Area of Science:
- Biochemistry
- Bioinformatics
- Computational Biology
Background:
- Protein phosphorylation is a crucial post-translational modification regulating cellular processes.
- Efficiently extracting and organizing phosphorylation data from scientific literature is challenging.
- Existing literature mining tools may lack specific focus on phosphorylation events.
Purpose of the Study:
- To develop a web-based literature mining system (RLIMS-P) for protein phosphorylation.
- To enable online extraction of phosphorylation information from MEDLINE abstracts.
- To facilitate the association of mined data with biological databases for enhanced analysis.
Main Methods:
- Development of a web-based platform for literature mining.
- Implementation of algorithms to extract phosphorylation objects: phosphorylated proteins, sites, and kinases.
- Integration with UniProt Knowledgebase for mapping phosphorylated proteins.
- Presentation of extracted data in summary tables and detailed reports with evidence tagging.
Main Results:
- Successful development and deployment of the RLIMS-P web tool.
- Extraction of key phosphorylation-related entities from MEDLINE abstracts.
- Automated mapping of identified proteins to UniProt entries.
- Generation of comprehensive reports detailing phosphorylation features and supporting evidence.
Conclusions:
- The RLIMS-P system provides an effective online solution for mining protein phosphorylation data.
- The tool enhances the retrieval of biological information for phosphorylated proteins.
- RLIMS-P facilitates efficient database annotation of phosphorylation-related features, supporting further research.
Related Concept Videos
02:54Protein Kinases and Phosphatases
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
02:26Protein Networks
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These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:04Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
02:04Covalently Linked Protein Regulators
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
These groups modify specific amino acids in a protein.