PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry
PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry
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DOI：
10.1111/j.1747-0285.2008.00661.x
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发表时间：
2008-06-01
影响因子：
3
通讯作者：
Meroueh, Samy O.
中科院分区：
文献类型：
--
作者：
Li, Liwei;Dantzer, Justin J.;Meroueh, Samy O.
由于熵-焓补偿，仅根据结构设计的化合物通常不会导致结合亲和力的任何改善。热力学数据和结构提供了深入了解这种效应的机会，并有助于细化计算药物设计中使用的评分函数。在这里，我们查阅了文献并构建了迄今为止最全面的手工量热数据集。它包含 400 多种受体-配体复合物的热力学和结构数据。该数据集可以通过 http://www.pdbcal.org 的 Web 界面访问。热力学数据包括通过等温滴定量热法 (ITC) 测量的自由能、焓、熵和热容。该数据集还包含用于进行 ITC 实验的实验条件。还提供了配体的化学结构。数据分析首次使用严格的ITC数据证实了熵-熵补偿效应的存在。
Compounds designed solely based on structure often do not result in any improvement of the binding affinity because of entropy - enthalpy compensation. Thermodynamic data along with structure provide an opportunity to gain a deeper understanding of this effect and aid in the refinement of scoring functions used in computational drug design. Here, we scoured the literature and constructed the most comprehensive handcurated calorimetry dataset to date. It contains thermodynamic and structural data for more than 400 receptor - ligand complexes. The dataset can be accessed through a web interface at http:// www.pdbcal.org. The thermodynamic data consists of free energy, enthalpy, entropy and heat capacity as measured by isothermal titration calorimetry (ITC). The dataset also contains the experimental conditions that were used to carry out the ITC experiments. The chemical structures of the ligands are also provided. Analysis of the data confirms the existence of enthalpy-entropy compensation effect for the first time using strictly ITC data.