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Related Concept Videos

Nuclear Localization Signals and Import01:46

Nuclear Localization Signals and Import

Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
Translation01:31

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life
Translation01:31

Translation

Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life
Proteins are called the...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Jun 2, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Modification site localization scoring integrated into a search engine.

Peter R Baker1, Jonathan C Trinidad, Robert J Chalkley

  • 1Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94158, USA.

Molecular & Cellular Proteomics : MCP
|April 15, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new scoring system for post-translational modification site assignments within the Protein Prospector search engine. This tool enhances the reliability of modification site identification in large proteomic datasets.

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An Automated System for Sound Localization Testing in Hearing-Impaired Listeners
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An Automated System for Sound Localization Testing in Hearing-Impaired Listeners

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Related Experiment Videos

Last Updated: Jun 2, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

An Automated System for Sound Localization Testing in Hearing-Impaired Listeners
07:52

An Automated System for Sound Localization Testing in Hearing-Impaired Listeners

Published on: March 13, 2026

Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Large-scale proteomic studies generate vast amounts of data with numerous modified peptides.
  • Assessing the reliability of peptide identifications is established, but confidence in modification site assignments remains a challenge.
  • Existing tools for modification site reliability are often external, limited in scope (e.g., phosphorylation only), and not integrated with search engines.

Purpose of the Study:

  • To develop and evaluate a novel site assignment scoring system integrated directly into the Protein Prospector search engine.
  • To provide automatic and reliable assessment of modification site assignments for all identified peptides.
  • To address the scarcity of tools for measuring confidence in post-translational modification site assignments.

Main Methods:

  • Integration of a site assignment scoring algorithm into the Protein Prospector software.
  • Development of a system to automatically report reliability scores for all modifications.
  • Implementation of clear indicators for ambiguous site assignments and the specific residues involved.

Main Results:

  • The integrated scoring system successfully reports site assignment reliability for all modifications within identified peptides.
  • The system automatically flags ambiguous assignments, specifying the potential residue locations.
  • An assignment score is generated, which can be converted into a quantitative measure of site assignment reliability.

Conclusions:

  • The integrated site assignment scoring in Protein Prospector offers a robust solution for assessing modification site reliability.
  • This approach automates the reporting of confidence levels, improving the analysis of post-translational modifications.
  • The tool enhances the interpretation of large-scale proteomic data by providing reliable site assignment measures.