関連する実験動画

Updated: Mar 22, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

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相互作用エントロピー:高効率で信頼性の高いタンパク質-リガンド結合自由エネルギーの計算のための新しいパラダイム

Lili Duan1,2, Xiao Liu1, John Z H Zhang1,3,4,5

  • 1Department of Physics, College of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.

Journal of the American Chemical Society
|April 10, 2016
PubMed
まとめ

新しい相互作用エントロピーの方法は,薬剤設計に不可欠なタンパク質-リガンド結合の自由エネルギーを計算する計算的に効率的で信頼性の高い方法を提供します. この方法は,従来のアプローチを上回る分子動力学シミュレーションからのエントロピー貢献を直接計算します.

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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.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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The Equilibrium Binding Constant and Binding Strength

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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Conserved Binding Sites

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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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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