Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs.,Mini-Reviews in Medicinal Chemistry

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Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs.
Mini-Reviews in Medicinal Chemistry ( IF 3.3 ) Pub Date : 2020-06-30 , DOI: 10.2174/1389557520666200526183353
K Kumar Reddy ₁ , R S Rathore ₂ , P Srujana ₂ , R R Burri ₃ , C Ravikumar Reddy ₄ , M Sumakanth ₅ , Pallu Reddanna ₁ , M Rami Reddy ₄

Affiliation

Background: The accurate ranking of analogs of lead molecules with respect to their estimated binding free energies to drug targets remains highly challenging in molecular docking due to small relative differences in their free energy values.

Methods: Free energy perturbation (FEP) method, which provides the most accurate relative binding free energy values were earlier used to calculate free energies of many ligands for several important drug targets including Fructose-1,6-BisphosPhatase (FBPase). The availability of abundant structural and experimental binding affinity data for FBPase inhibitors provided an ideal system to evaluate four widely used docking programs, AutoDock, Glide, GOLD and SurflexDock, distinct from earlier comparative evaluation studies.

中文翻译：

使用自由能摄动参考数据对接程序（Glide，GOLD，AutoDock和SurflexDock）的性能评估：以果糖-1、6-双磷酸酶-AMP类似物为例。

背景：铅分子类似物相对于其与药物靶标的估计结合自由能的准确排名在分子对接中仍然具有很高的挑战性，因为它们的自由能值相对较小。

方法：提供最准确的相对结合自由能值的自由能扰动（FEP）方法已被较早地用于计算几个重要药物靶标（包括果糖1,6-双歧磷酸酶（FBPase））的许多配体的自由能。FBPase抑制剂丰富的结构和实验结合亲和力数据的可用性为评估四种广泛使用的对接程序（AutoDock，Glide，GOLD和SurflexDock）提供了理想的系统，这与早期的比较评估研究不同。

更新日期：2020-07-27

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