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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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A Basic Protein Comparative Three-Dimensional Modeling Methodological Workflow Theory and Practice.

Mainá Bitar, Glória Regina Franco

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |September 11, 2015
    PubMed
    Summary
    This summary is machine-generated.

    This guide explains comparative modeling for protein structure prediction when experimental data is unavailable. It details essential bioinformatics techniques for generating accurate in silico protein models.

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    Area of Science:

    • Bioinformatics
    • Structural Biology
    • Computational Chemistry

    Background:

    • Access to three-dimensional protein structures is vital for studying molecular properties.
    • Experimentally determined structures are not always available, necessitating alternative methods.
    • Bioinformatics is increasingly central to protein structure research, requiring clear methodological guidance.

    Purpose of the Study:

    • To provide a comprehensive overview of comparative modeling techniques for protein structure prediction.
    • To detail the algorithms and theoretical underpinnings of comparative modeling.
    • To offer a practical, step-by-step workflow for biologists performing in silico protein structure generation.

    Main Methods:

    • Exploration of comparative modeling steps: template identification, sequence alignment, candidate structure generation, and quality assessment.
    • Theoretical description of the peculiarities and algorithms involved in each step.
    • Presentation of a practical, guided workflow for in silico protein structure generation.

    Main Results:

    • Detailed explanation of the comparative modeling process, including its theoretical basis.
    • A structured, step-by-step protocol designed to assist biologists in generating protein models.
    • Identification of further perspectives in protein structure study using bioinformatics.

    Conclusions:

    • Comparative modeling is a valuable technique for generating protein structure models when experimental data is lacking.
    • The provided workflow serves as a thorough guide for beginners in protein comparative modeling.
    • Bioinformatics offers expanding possibilities for advancing the study of protein structures.