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Related Concept Videos

Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Covalently Linked Protein Regulators02:04

Covalently 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.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Mutations01:39

Mutations

Overview
Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...

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Articles linked to this work by shared authors, journal, and citation graph.

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Evaluation of a combined tuberculosis case-finding, treatment and prevention strategy in Thailand: protocol for a pragmatic phase IV stepped-wedge cluster-randomised trial, the CaPThai study.

Trials·2026
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Bedaquiline, delamanid, linezolid, and clofazimine for rifampicin-resistant and fluoroquinolone-resistant tuberculosis (endTB-Q): an open-label, multicentre, stratified, non-inferiority, randomised, controlled, phase 3 trial.

The Lancet. Respiratory medicine·2025
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The Effectiveness and Safety of Bedaquiline, Pretomanid, and Linezolid (BPaL)-Based Regimens for Rifampicin-Resistant Tuberculosis in Non-Trial Settings-A Prospective Cohort Study in Belarus and Uzbekistan.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America·2025
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Oral Regimens for Rifampin-Resistant, Fluoroquinolone-Susceptible Tuberculosis.

The New England journal of medicine·2025
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Characteristics of children and adolescents with multidrug-resistant and rifampicin-resistant tuberculosis and their association with treatment outcomes: a systematic review and individual participant data meta-analysis.

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The Frequency and Incidence of QT Prolongation With Extended Use of Bedaquiline or Delamanid in a Large, Multi-Country Multidrug-Resistant/Rifampicin-Resistant Tuberculosis Cohort.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America·2024

Related Experiment Video

Updated: Jul 8, 2026

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Retrieving mutation-specific information for human proteins in UniProt/Swiss-Prot Knowledgebase.

Yum Lina Yip1, Nathalie Lachenal, Violaine Pillet

  • 1Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1, rue Michel-Servet, 1211, Geneva 4, Switzerland. lina.yip@isb-sib.ch

Journal of Bioinformatics and Computational Biology
|January 4, 2008
PubMed
Summary

An automated method efficiently retrieves scientific articles on single amino acid polymorphisms (SAPs). This approach enhances the Swiss-Prot database by keeping variant information current and accessible to researchers.

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
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Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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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

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Genomics
  • Proteomics

Background:

  • The UniProt/Swiss-Prot Knowledgebase documents over 30,500 protein variants, primarily single amino acid polymorphisms (SAPs).
  • Maintaining an up-to-date literature record for these SAPs is crucial for biological research.

Purpose of the Study:

  • To develop an automated information retrieval method for identifying published texts that mention SAPs.
  • To improve the accessibility and currency of variant information in the Swiss-Prot database.

Main Methods:

  • Developed an automated method using regular expressions and rules for detecting and validating mutations.
  • Applied the method to retrieve articles on 5,664 proteins with variants by querying PubMed with gene/protein names and mutation keywords.
  • Incorporated nonstandard mutation nomenclature and sequence positional correction for enhanced retrieval accuracy.

Main Results:

  • The automated retrieval method achieved a precision of 89.5% across a corpus of 9,820 PubMed references.
  • The method demonstrated efficiency in identifying new references related to known polymorphisms.
  • The approach successfully recovered relevant documents, including those with nonstandard mutation descriptions.

Conclusions:

  • The developed automated method is effective for updating literature records on SAPs.
  • This system will ensure that new references on known SAPs are promptly made available through Swiss-Prot variant pages.
  • The findings highlight the importance of handling diverse mutation nomenclature for comprehensive literature mining.