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Ligand Binding Sites

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...

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

The Equilibrium Binding Constant and Binding Strength

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:

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

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関連する実験動画

Updated: Feb 17, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

マクロサイクリックリガンドの正確な物理ベースの柔軟なドッキング

Jacob Robson-Tull¹, João P G L M Rodrigues¹

¹Schrodinger New York, 1540 Broadway, 24th Floor, New York, New York 10035, United States.

Journal of medicinal chemistry

|February 16, 2026

まとめ

新しいコンピューティングモデリングプロトコルは,マクロサイクルの薬剤発見の精度を高めています. この柔軟なドッキング方法は,マクロサイクル化合物が標的に結合する方法を効果的に予測し,構造ベースの治療開発を改善します.

科学分野:

計算化学はコンピュータ化学である.
薬剤化学薬剤化学について
ドラッグ・ディスカバリー・ドラッグ・ディスカバリー

背景:

マクロサイクルは,コンピューティングモデリングの課題に直面する重要な治療クラスです.
既存の方法は,サンプル採取のバイオアクティブ構造と結合モードの予測に苦労しています.
これらの制限は,マクロサイクリック療法のための構造ベースの薬剤発見を妨げています.

研究の目的:

マクロサイクルのための改善されたコンピューティングドッキングプロトコルの開発.
マクロサイクルの結合モードと構成を予測する精度を高めるために.
現在のマクロサイクルモデリング技術の限界を克服するために.

主な方法:

新しい柔軟なマクロサイクルのドッキングプロトコルを開発しました.
統合された既存のシュレーディンガーマクロサイクルサンプリングと小分子ドッキング技術.
240の受容体マクロサイクルシステムの拡張されたデータセットを使用してプロトコルをベンチマークしました.

主要な成果:

新しいプロトコルは,既存のドッキングツールを大幅に上回ります.
トップ2ポジション内での受容体結合構造の再構成で82%の精度を達成しました.

さらに関連する動画

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

関連する実験動画

Last Updated: Feb 17, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

いくつかの臨床的に重要なマクロサイクル化合物の結合を成功裏にモデル化しました.

結論:

開発された柔軟なマクロサイクルのドッキングプロトコルは,構造ベースの薬剤発見の有意な約束を示しています.
この方法は,マクロサイクルの結合姿勢と形状の予測を改善します.
マクロサイクルモデリングにおける誘導フィット効果とストレスのような課題に対処するために,さらなる研究が必要である.