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Related Concept Videos

Protein Modifications in the RER01:26

Protein Modifications in the RER

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
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In statistics, several tools are used to interpret the data. Measures of central tendency represent the characteristics of the data, such as mean, median, and mode. Additionally, measures of variance like standard deviation and range are used to find the spread of data from the mean. Relative standing measures the distance between data locations. Commonly used measures of relative standings are percentile, z score, and quartiles.
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Data are individual items of information obtained from a population or sample. Data may be classified as qualitative (categorical), quantitative continuous, or quantitative discrete. Because it is not practical to measure the entire population in a study, researchers use samples to represent the population. A random sample is a representative group from the population chosen by using a method that gives each individual in the population an equal chance of being included in the sample. Random...
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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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A problem-solving strategy is a plan of action used to find a solution. Different strategies have distinct action plans. Trial and error involves trying different solutions until one works. For instance, to fix a broken printer, you might check ink levels, ensure the paper tray isn't jammed, and verify the printer's connection to your laptop. This method can be time-consuming but is commonly used. Thomas Edison, for example, used trial and error to find a suitable filament for the light...
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A Systematic Review on Posttranslational Modification in Proteins: Feature Construction, Algorithm and Webserver.

Yan Xu1, Yingxi Yang1, Zu Wang1

  • 1Department of Information and Computer Science, University of Science and Technology Beijing, Beijing 100083, China.

Protein and Peptide Letters
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Summary
This summary is machine-generated.

Identifying post-translational modification (PTM) sites in proteins is crucial for research and drug design. This review details computational methods for predicting PTM sites, offering a convenient alternative to laborious experimental techniques.

Keywords:
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Post-translational modifications (PTMs) are vital for protein functions and biological processes.
  • Identifying PTM sites is significant for basic research and drug design.
  • Experimental PTM identification is time-consuming; computational methods offer a convenient alternative.

Purpose of the Study:

  • To review computational approaches for predicting post-translational modification sites in proteins.
  • To cover feature construction, algorithms, evaluation metrics, and web servers for PTM site prediction.
  • To discuss strategies for predicting both single and crosstalk PTM sites.

Main Methods:

  • Feature construction for protein sequences.
  • Application of machine learning algorithms (binary classification for single PTMs, multi-label learning for crosstalk PTMs).
  • Evaluation of prediction performance using established metrics.

Main Results:

  • Computational methods provide a viable and convenient approach for PTM site identification.
  • Different machine learning strategies are effective for single vs. crosstalk PTM site prediction.
  • The review consolidates key steps and considerations in developing PTM prediction tools.

Conclusions:

  • This review summarizes the workflow for predicting post-translational modification sites.
  • It highlights the transformation of PTM prediction into classification and multi-label learning problems.
  • The discussed methods and tools aid in advancing PTM site identification for biological research and drug discovery.