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Protein Organization01:24

Protein Organization

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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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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.

Zhiquan He, Chao Zhang, Yang Xu

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    |January 7, 2015
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    Summary

    MUFOLD-DB offers cleaned, non-redundant protein structure data from the Protein Data Bank (PDB). This database addresses data redundancy and quality issues, aiding protein research and structure prediction.

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    Area of Science:

    • Structural biology
    • Bioinformatics
    • Computational biology

    Background:

    • Protein Data Bank (PDB) data is crucial for protein function, evolution, and prediction studies.
    • Large-scale PDB data usage is hindered by sequence/structure redundancy and data inconsistencies, including missing residues.
    • These issues complicate automated data retrieval and analysis.

    Purpose of the Study:

    • To create a comprehensive, user-friendly database of processed Protein Data Bank (PDB) data.
    • To provide non-redundant, cleaned, and enhanced protein structure information.
    • To facilitate large-scale analysis and understanding of protein structures.

    Main Methods:

    • Developed MUFOLD-DB, a web-based database processing weekly PDB files.
    • Collected and cleaned PDB data, ensuring non-redundancy.
    • Annotated SCOP domain classification and predicted missing protein regions using loop modeling.
    • Computed and visualized evolutionary information, secondary structure, and disorder regions.

    Main Results:

    • MUFOLD-DB provides non-redundant, cleaned, and partially-predicted protein structure data.
    • Includes SCOP domain classifications and predicted structures for missing regions.
    • Offers integrated evolutionary information, secondary structure, and disorder region data.
    • Processed 3D structures are computed and visualized for enhanced user understanding.

    Conclusions:

    • MUFOLD-DB integrates processed PDB data with computational results for easier access.
    • Features a user-friendly interface for data retrieval, browsing, and downloading.
    • Provides functionalities to support and facilitate user data operations in protein research.