Development of CDK-targeted scoring functions for prediction of binding affinity

Bernhardt Levin Nayara Maria; Pintro Val Oliveira; Bitencourt-Ferreira Gabriela; de Mattos Bruna Boldrini; Silverio Ariadne de Castro; de Azevedo Walter Filgueira Jr.

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Development of CDK-targeted scoring functions for prediction of binding affinity

机译：开发CDK目标评分函数，用于预测结合亲和力

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摘要

Cyclin-dependent kinase (CDK) is an interesting biological macromolecule due to its role in cell cycle progression, transcription control, and neuronal development, to mention the most studied biological activities. Furthermore, the availability of hundreds of structural studies focused on the intermolecular interactions of CDK with competitive inhibitors makes possible to develop computational models to predict binding affinity, where the atomic coordinates of binary complexes involving CDK and ligands can be used to train a machine learning model. The present work is focused on the development of new machine learning models to predict binding affinity for CDK. The CDK-targeted machine learning models were compared with classical scoring functions such as MolDock, AutoDock 4, and Vina Scores. The overall performance of our CDK-targeted scoring function was higher than the previously mentioned scoring functions, which opens the possibility of increasing the reliability of virtual screening studies focused on CDK.

机译：Cyclin依赖性激酶（CDK）是一种有趣的生物大分子，因为它在细胞周期进展，转录控制和神经元发展中的作用，提及最多研究的生物活性。此外，对具有竞争性抑制剂的CDK的分子间相互作用的数百种结构研究可以实现用于预测结合亲和力的计算模型，其中涉及CDK和配体的二元复合物的原子坐标可用于训练机器学习模型。本工作专注于开发新机器学习模型，以预测CDK的结合亲和力。将CDK目标机器学习模型与莫莫克，自动汇集4和vina分数等经典评分功能进行了比较。我们的CDK目标评分功能的整体性能高于前面提到的评分功能，这使得增加了增加专注于CDK的虚拟筛选研究的可靠性的可能性。

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来源
《Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena》 |2018年第2018期|共8页
作者
Bernhardt Levin Nayara Maria; Pintro Val Oliveira; Bitencourt-Ferreira Gabriela; de Mattos Bruna Boldrini; Silverio Ariadne de Castro; de Azevedo Walter Filgueira Jr.;
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作者单位

Pontifcia Catholic Univ Rio Grande Sul PUCRS Sch Sci Lab Computat Syst Biol Av Ipiranga 6681 BR;

Pontifcia Catholic Univ Rio Grande Sul PUCRS Sch Sci Lab Computat Syst Biol Av Ipiranga 6681 BR;

Pontifcia Catholic Univ Rio Grande Sul PUCRS Sch Sci Lab Computat Syst Biol Av Ipiranga 6681 BR;

Pontifcia Catholic Univ Rio Grande Sul PUCRS Sch Sci Lab Computat Syst Biol Av Ipiranga 6681 BR;

Pontifcia Catholic Univ Rio Grande Sul PUCRS Sch Sci Lab Computat Syst Biol Av Ipiranga 6681 BR;

Pontifcia Catholic Univ Rio Grande Sul PUCRS Sch Sci Lab Computat Syst Biol Av Ipiranga 6681 BR;

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原文格式 PDF
正文语种 eng
中图分类生物化学;
关键词
Bioinformatics; Machine learning; CDK; Drug design; Docking; Protein;

机译：生物信息学;机器学习;CDK;药物设计;对接;蛋白质;

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Development of CDK-targeted scoring functions for prediction of binding affinity

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