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Related Concept Videos

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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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Related Experiment Video

Updated: Jul 3, 2026

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

BCL::Align-sequence alignment and fold recognition with a custom scoring function online.

Elizabeth Dong1, Jarrod Smith, Sten Heinze

  • 1Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.

Gene
|July 8, 2008
PubMed
Summary
This summary is machine-generated.

BCL::Align offers superior multiple sequence alignment and protein fold recognition by combining dynamic programming with a flexible, customizable scoring function. Optimized weights enhance accuracy, outperforming other leading tools in benchmark tests.

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Last Updated: Jul 3, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
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16:41

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09:51

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

Published on: July 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding protein evolution and function.
  • Accurate protein fold recognition is essential for predicting structure and function.
  • Existing MSA tools have limitations in accuracy and flexibility.

Purpose of the Study:

  • To develop a novel multiple sequence alignment tool, BCL::Align.
  • To create a customizable scoring function for enhanced sequence alignment and fold recognition.
  • To optimize BCL::Align for various protein classes and fold families.

Main Methods:

  • Utilized dynamic programming for sequence alignment.
  • Developed a scoring function integrating PAM, BLOSUM, PSI-BLAST matrices, predicted secondary structures, chemical properties, and gap penalties.
  • Employed a Monte Carlo algorithm to optimize scoring function weights.
  • Evaluated performance using the SABmark reference alignment test set.

Main Results:

  • BCL::Align achieved the highest alignment accuracy (Cline score 22.90) for sequences in the Twilight Zone, surpassing Align-m, ClustalW, T-Coffee, and MUSCLE.
  • Achieved over 80% accuracy in protein fold recognition, as indicated by ROC curve analysis.
  • Demonstrated flexibility for optimization on specific protein classes (e.g., membrane proteins) and fold families (e.g., TIM-barrel proteins).

Conclusions:

  • BCL::Align provides a highly accurate and flexible solution for multiple sequence alignment and fold recognition.
  • The customizable scoring function allows tailoring the tool for specific bioinformatics tasks.
  • BCL::Align represents a significant advancement in computational tools for protein sequence and structure analysis.