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Related Concept Videos

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Networks02:26

Protein Networks

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.
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,...
Protein-protein Interfaces02:04

Protein-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...
Protein-Protein Interfaces02:04

Protein-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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Improvements in the Protein Identifier Cross-Reference service.

Samuel P Wein1, Richard G Côté, Marine Dumousseau

  • 1EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Nucleic Acids Research
|May 1, 2012
PubMed
Summary

The Protein Identifier Cross-Reference (PICR) service enhances protein and gene data mapping across 102 databases. New features improve cross-database identifier resolution for researchers.

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The Protein Identifier Cross-Reference (PICR) service facilitates mapping of protein and gene identifiers.
  • It supports diverse input and output formats, including web, REST, and SOAP services.
  • PICR has been operational since 2007, supporting cross-database data integration.

Purpose of the Study:

  • To describe the recent enhancements and expanded functionality of the PICR service.
  • To detail the integration of new databases and improved mapping algorithms.
  • To highlight the increased utility of PICR for bioinformatics research.

Main Methods:

  • Implemented new functionalities including Basic Local Alignment Search Tool (BLAST) for protein subsequences against UniProt Knowledgebase (UniProtKB).
  • Integrated gene identifier mapping for UniProtKB and Ensembl, supporting both input and output.
  • Developed a 'best-guess' mapping algorithm for UniProt data.
  • Expanded database coverage from 73 to 102 sources, including new Ensembl databases.

Main Results:

  • PICR now covers 102 databases, an increase from 73.
  • Enhanced capabilities include BLAST searches and improved gene identifier mapping.
  • New species-specific Ensembl databases and Ensembl Genome databases have been added.
  • Web services have been updated to reflect new functionalities.

Conclusions:

  • The enhanced PICR service offers significantly improved protein and gene identifier mapping capabilities.
  • Increased database coverage and new algorithms provide researchers with more comprehensive cross-referencing tools.
  • PICR remains a valuable resource for bioinformatics, facilitating data integration and analysis across diverse biological databases.