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Protein and Protein Structure02:15

Protein and Protein Structure

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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Protein Folding Quality Check in the RER01:29

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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 Domains02:26

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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.
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Updated: Jun 14, 2026

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

Feedback algorithm and web-server for protein structure alignment.

Zhiyu Zhao1, Bin Fu, Francisco J Alanis

  • 1Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA. zzha2@cs.uno.edu

Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference
|August 1, 2009
PubMed
Summary
This summary is machine-generated.

A new feedback algorithm for protein structure alignment improves alignment accuracy. This method, available online, offers more aligned positions and smaller root-mean-square deviation (RMSD) for weak structural similarities.

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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
05:08

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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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Protein structure alignment is crucial for understanding protein function and evolution.
  • Existing algorithms have limitations in accurately aligning homologous and analogous protein structures, especially when structural similarity is low.

Purpose of the Study:

  • To develop and evaluate a novel feedback algorithm for protein backbone structure alignment.
  • To compare the performance of the new algorithm against established methods like CE, DaliLite, and SSM.
  • To provide a freely accessible web portal for utilizing the developed alignment method.

Main Methods:

  • Development of a feedback algorithm incorporating learning principles for protein structure alignment.
  • Implementation of the algorithm into a web portal for public access.
  • Comparative analysis against CE, DaliLite, and SSM using metrics such as (Calpha) RMSD and the number of aligned positions.

Main Results:

  • The developed algorithm consistently produced a larger number of aligned positions compared to CE, DaliLite, and SSM at comparable (Calpha) RMSD values.
  • In numerous instances, the algorithm achieved a smaller (Calpha) RMSD than the other methods when the number of aligned positions was similar or greater.
  • These improvements were particularly pronounced in cases involving proteins with weak structural similarities.

Conclusions:

  • The new feedback algorithm offers superior performance in protein structure alignment, particularly for distantly related proteins.
  • The developed web portal provides a valuable resource for researchers to leverage this advanced alignment tool.
  • The findings suggest that feedback-driven approaches can enhance the accuracy and reliability of protein structure comparisons.