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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...
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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Conservation of Protein Domains Over Different Proteins02:26

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Related Experiment Video

Updated: May 11, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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T-RMSD: a web server for automated fine-grained protein structural classification.

Cedrik Magis1, Paolo Di Tommaso, Cedric Notredame

  • 1Bioinformatics and Genomics Programme, Centre For Genomic Regulation, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.

Nucleic Acids Research
|May 30, 2013
PubMed
Summary
This summary is machine-generated.

The T-RMSD web server provides online protein classification using tree-based root-mean-square deviation (RMSD) analysis. It reveals structural and functional relationships within protein families by clustering proteins based on structural similarity.

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Last Updated: May 11, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Understanding protein structure-function relationships is crucial in biology.
  • Existing methods may lack the resolution for fine-grained structural classification.
  • Computational tools are needed to analyze large protein datasets efficiently.

Purpose of the Study:

  • To introduce the T-RMSD web server for online, structure-based protein classification.
  • To enable fine-grained structural clustering of protein families.
  • To quantitatively assess structural and functional similarity in proteins.

Main Methods:

  • Utilizing tree-based root-mean-square deviation (RMSD) analysis.
  • Computing distance RMSD (dRMSD) variations between equivalent residues.
  • Generating distance matrices and constructing a structural tree with support values.

Main Results:

  • The T-RMSD server enables online computation of protein classification.
  • It provides a quantitative estimate of structural distances using tree topology.
  • Generated clusters are informative of both structural and functional protein properties.

Conclusions:

  • The T-RMSD web server offers a valuable tool for analyzing protein structural diversity.
  • It facilitates the discovery of structure-function relationships within protein families.
  • The server provides a user-friendly platform for researchers in structural bioinformatics.