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Related Concept Videos

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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Updated: Jun 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation.

Russell J Dickson1, Lindi M Wahl, Andrew D Fernandes

  • 1Department of Biochemistry, The University of Western Ontario, London, Canada.

Plos One
|July 3, 2010
PubMed
Summary
This summary is machine-generated.

Current methods cannot verify protein alignment quality. New covariation statistics can identify alignment errors and improve contact prediction, offering a more reliable verification step for sequence alignments.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Last Updated: Jun 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

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

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Published on: July 12, 2022

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Traditional criteria for evaluating multiple sequence alignments are insufficient and assumption-dependent.
  • Covariation analysis, used for identifying important residue pairs, is highly sensitive to the quality of sequence alignments.
  • Existing methods lack a robust, independent way to verify the accuracy of protein sequence alignments.

Purpose of the Study:

  • To demonstrate that current protein alignment evaluation criteria are insufficient for covariation analyses.
  • To show that covariation analysis can be used to detect systematic errors in sequence alignments.
  • To develop and present novel covariation statistics that are more robust to alignment errors.

Main Methods:

  • Systematic evaluation of sequence alignment errors in curated datasets.
  • Analysis of the sensitivity of non-parametric covariation statistics to sequence misalignments.
  • Development of new non-parametric statistics emphasizing pairwise covariation.

Main Results:

  • Systematic alignment errors exist even in high-quality, curated protein alignment datasets.
  • Non-parametric covariation statistics are sensitive to alignment errors, which can be exploited for error detection.
  • Removing alignment errors (e.g., from improper structure alignment, paralogs, or erroneous sequences) significantly improves contact prediction accuracy.
  • Two new non-parametric covariation statistics demonstrate reduced sensitivity to alignment errors.

Conclusions:

  • Errors in protein alignments lead to inaccurate conclusions regarding residue covariation and conservation.
  • Covariation analysis serves as a valuable, independent verification method for identifying systematic misalignments in protein sequence alignments.
  • The newly developed non-parametric statistics enhance confidence in contact prediction, particularly in alignments containing erroneous regions.