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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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Protein Organization01:13

Protein Organization

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Overview
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Protein and Protein Structure02:15

Protein and Protein Structure

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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.
A protein's shape is critical to its function. For example, an enzyme...
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Protein and Protein Structures02:15

Protein and Protein Structures

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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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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Updated: Mar 15, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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Recent advances in sequence-based protein structure prediction.

Dukka B Kc

    Briefings in Bioinformatics
    |August 27, 2016
    PubMed
    Summary
    This summary is machine-generated.

    Computational protein structure prediction is crucial as experimental methods are costly. Free modeling (FM) approaches are advancing rapidly, generating accurate protein models without templates, as seen in recent competitions.

    Keywords:
    CASPcontact predictionevolutionary constraintsfree modelingprotein structure predictiontemplate-based modeling

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    Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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    A Protocol for Computer-Based Protein Structure and Function Prediction
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    Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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    Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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    Area of Science:

    • Computational Biology
    • Structural Biology
    • Bioinformatics

    Background:

    • Experimental protein structure determination is accurate but expensive and slow.
    • A widening gap exists between the number of known protein sequences and experimentally solved structures.
    • Computational protein structure prediction is vital for biological research.

    Purpose of the Study:

    • To highlight progress in computational protein structure prediction.
    • To focus on free modeling (FM) methods that predict structures without homologous templates.
    • To review recent advances, competition results, and future trends in FM approaches.

    Main Methods:

    • Review of recent advancements in free modeling (FM) techniques for protein structure prediction.
    • Analysis of performance in the Computational Assessment of Structure Prediction (CASP) competition.
    • Discussion of trends and future outlook for template-free protein modeling.

    Main Results:

    • Significant progress has been made in free modeling (FM) approaches for protein structure prediction.
    • Recent CASP competitions demonstrate the increasing accuracy of FM methods.
    • FM methods are becoming a powerful tool for modeling protein structures from sequences.

    Conclusions:

    • Computational methods, particularly FM, are essential for bridging the sequence-structure gap.
    • Continued development in FM promises to accelerate biological discovery.
    • The field is rapidly evolving, with promising trends for future protein structure prediction.