化学
计算机科学
卷积神经网络
Web服务器
药物发现
过程(计算)
图形
人工智能
化学
深度学习
数据挖掘
机器学习
理论计算机科学
互联网
程序设计语言
万维网
生物化学
作者
Xiaolin Pan,Hao Wang,Cuiyu Li,John Z. H. Zhang,Changge Ji
标识
DOI:10.1021/acs.jcim.1c00075
摘要
pKa is an important property in the lead optimization process since the charge state of a molecule in physiologic pH plays a critical role in its biological activity, solubility, membrane permeability, metabolism, and toxicity. Accurate and fast estimation of small molecule pKa is vital during the drug discovery process. We present MolGpKa, a web server for pKa prediction using a graph-convolutional neural network model. The model works by learning pKa related chemical patterns automatically and building reliable predictors with learned features. ACD/pKa data for 1.6 million compounds from the ChEMBL database was used for model training. We found that the performance of the model is better than machine learning models built with human-engineered fingerprints. Detailed analysis shows that the substitution effect on pKa is well learned by the model. MolGpKa is a handy tool for the rapid estimation of pKa during the ligand design process. The MolGpKa server is freely available to researchers and can be accessed at https://xundrug.cn/molgpka.
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