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Related Concept Videos

Protein Organization01:24

Protein Organization

9.9K
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....
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein Folding01:22

Protein Folding

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Overview
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Predicting Molecular Geometry02:27

Predicting Molecular Geometry

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VSEPR Theory for Determination of Electron Pair Geometries
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Amyloid Fibrils03:03

Amyloid Fibrils

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Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
Amyloid deposits were observed as early as 1639 in the liver and the spleen.   In 1854, Rudolph Virchow performed iodine staining,...
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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A Memetic Algorithm for 3-D Protein Structure Prediction Problem.

Leonardo Correa, Bruno Borguesan, Camilo Farfan

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |December 8, 2016
    PubMed
    Summary
    This summary is machine-generated.

    This study introduces a novel Memetic Algorithm for 3D protein structure prediction, leveraging domain knowledge to efficiently find native-like protein structures. The approach integrates Simulated Annealing and Protein Data Bank insights for improved accuracy.

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    Area of Science:

    • Computational Biology
    • Bioinformatics
    • Artificial Intelligence

    Background:

    • Protein structure prediction is crucial for understanding biological function.
    • Accurate prediction remains a significant challenge in computational biology.
    • Existing methods often struggle with complex protein folding dynamics.

    Purpose of the Study:

    • To develop and evaluate a novel Memetic Algorithm for accurate three-dimensional protein structure prediction.
    • To incorporate problem-specific domain knowledge into the metaheuristic search process.
    • To improve the efficiency and effectiveness of protein folding simulations.

    Main Methods:

    • A structured population Memetic Algorithm was designed.
    • Simulated Annealing was employed as a local search strategy.
    • Angle Probability Lists derived from the Protein Data Bank were used to guide the search.
    • Ad-hoc crossover and mutation operators were developed for protein sequences.

    Main Results:

    • The algorithm successfully predicted native-like protein structures for nineteen test sequences.
    • Results showed competitive root-mean-square deviation and global distance total scores.
    • The folding organization of predicted structures was comparable to state-of-the-art methods.

    Conclusions:

    • The proposed Memetic Algorithm effectively utilizes domain knowledge for protein structure prediction.
    • The integration of Simulated Annealing and Angle Probability Lists enhances search efficiency.
    • The algorithm demonstrates significant potential for advancing computational protein folding research.