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Updated: May 17, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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LIGYSIS-web:一种用于分析蛋白质 - 配体结合点的资源

Javier S Utgés1, Stuart A MacGowan1, Geoffrey J Barton1

  • 1Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH Scotland, UK.

Nucleic acids research
|May 16, 2025
PubMed
概括

LIGYSIS-web是一个免费的,可访问的在线工具,用于分析蛋白质-配体结合位点. 它使用进化,遗传和可访问性数据来预测功能重要性,帮助研究人员了解分子相互作用.

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Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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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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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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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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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
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