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Related Concept Videos

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 Networks02:26

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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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.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Cross-Species Protein Function Prediction with Asynchronous-Random Walk.

Yingwen Zhao, Jun Wang, Maozu Guo

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |September 29, 2019
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    Summary
    This summary is machine-generated.

    This study introduces Asynchronous Random Walk (AsyRW), a novel method for cross-species protein function prediction. AsyRW effectively leverages complementary annotations between species to significantly improve prediction accuracy.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Protein function prediction is crucial in genomics, but existing annotations are often incomplete.
    • Homologous species offer complementary functional information, yet methods to integrate this are underdeveloped.

    Purpose of the Study:

    • To develop an effective approach for cross-species protein function prediction by leveraging complementary annotations.
    • To improve the accuracy and performance of protein function prediction using heterogeneous biological data.

    Main Methods:

    • Constructed a heterogeneous network integrating various biological data, homology relationships, and Gene Ontology (GO) annotations.
    • Developed Asynchronous Random Walk (AsyRW) incorporating species-specific and GO structure information.
    • Quantified individual node walk lengths using gravity-like theory for asynchronous random walks.

    Main Results:

    • AsyRW effectively utilizes complementary annotations from different species.
    • The method demonstrates significantly improved performance compared to existing approaches.
    • Experiments confirm the efficacy of individual walk length and asynchronous random walks.

    Conclusions:

    • AsyRW provides a powerful framework for cross-species protein function prediction.
    • The approach successfully addresses the challenge of incomplete annotations by integrating complementary data.
    • The proposed method offers a substantial advancement in the field of bioinformatics.