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Related Concept Videos

Protein Organization01:24

Protein Organization

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.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
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...
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.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview

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Related Experiment Video

Updated: May 21, 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

Enhancement of initial equivalency for protein structure alignment based on encoded local structures.

Kenneth Hung, Jui-Chih Wang, Cheng-Wei Chen

    IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society
    |June 22, 2012
    PubMed
    Summary

    MIRAGE-align improves protein structure alignment by enhancing initial alignment quality using local structural features. This novel vector-based approach, accounting for low sequence identity pairs, outperforms existing methods and enables efficient non-iterative optimization.

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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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    Last Updated: May 21, 2026

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

    Published on: July 14, 2015

    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

    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

    Published on: July 8, 2025

    Area of Science:

    • Computational biology
    • Bioinformatics
    • Structural bioinformatics

    Background:

    • Protein structure alignment is crucial for understanding protein function and evolution.
    • Current alignment algorithms often rely on iterative optimization, which can be trapped in local optima due to poor initial alignments.
    • Identifying reliable alignments for proteins with low sequence identity (twilight zone) remains a challenge.

    Purpose of the Study:

    • To develop a novel vector-based protein structure alignment algorithm, MIRAGE-align.
    • To introduce an improved initial alignment strategy that incorporates local structural features.
    • To enhance the accuracy and efficiency of protein structure alignment, particularly for proteins with low sequence identity.

    Main Methods:

    • Proposed MIRAGE-align, a vector-based alignment algorithm.
    • Implemented a new initial alignment approach using encoded local structural alphabets.
    • Focused on identifying protein structure pairs in the twilight zone of sequence identity.
    • Performed statistical analysis using Match Index (MI) and computation time.

    Main Results:

    • MIRAGE-align demonstrated superior performance compared to CE, SSM, TM-align, and Fr-TM-align.
    • The algorithm provides a better estimate for the initial alignment solution.
    • Enhanced initial alignment quality allows for effective non-iterative optimization.

    Conclusions:

    • MIRAGE-align significantly improves protein structure alignment quality.
    • The novel initial alignment strategy effectively addresses challenges with low sequence identity.
    • MIRAGE-align offers a more efficient and accurate approach to protein structure alignment.