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Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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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...
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Protein Networks02:26

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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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...
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Phosphorylation01:02

Phosphorylation

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The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
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Covalently Linked Protein Regulators

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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.
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Text Mining and Machine Learning Protocol for Extracting Human-Related Protein Phosphorylation Information from

Krishnamurthy Arumugam1, Raja Ravi Shanker2

  • 1Department of Management Studies, Coimbatore Institute of Engineering and Technology, Coimbatore, Tamilnadu, India. kmurthya@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|June 17, 2022
PubMed
Summary

Automated text mining effectively extracts human protein phosphorylation data from biomedical literature. This approach uses natural language processing and machine learning to advance disease research.

Keywords:
Machine learningNatural language parsingProtein phosphorylationSupport vector machineText mining

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Protein phosphorylation is crucial for cellular communication and understanding human evolution.
  • Massive datasets on protein modifications necessitate automated data processing.
  • Extracting specific biological information from unstructured text is challenging.

Purpose of the Study:

  • To outline a text mining protocol for extracting human protein phosphorylation information.
  • To apply natural language parsing and machine learning for data analysis.
  • To evaluate the text mining system's performance on relevant corpora.

Main Methods:

  • Utilized natural language parsing (NLP) for named entity recognition and text processing.
  • Employed support vector machines (SVM) for text classification.
  • Evaluated the system on three distinct corpora: hPP, iProLink, and PLC.

Main Results:

  • Developed and evaluated a text mining protocol for human protein phosphorylation.
  • Demonstrated the application of NLP and SVM in processing biomedical literature.
  • Assessed system performance across multiple specialized corpora.

Conclusions:

  • The developed text mining protocol effectively extracts protein phosphorylation data.
  • This automated approach aids in managing and analyzing large biological datasets.
  • Understanding the underlying chemistry and biology can further enhance text mining systems for biomedical research.