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Updated: Jul 5, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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DeepRank-GNN-esm:使用蛋白质语言模型的蛋白质蛋白质模型评分图形神经网络

Xiaotong Xu1, Alexandre M J J Bonvin1

  • 1Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Utrecht 3584 CS, The Netherlands.

Bioinformatics advances
|January 12, 2024
PubMed
概括

DeepRank-GNN-esm通过用高效的蛋白质语言模型嵌入来取代计算上昂贵的PSSM功能来增强蛋白质-蛋白质相互作用建模,提高可用性和性能.

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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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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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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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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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