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高精度溶解度预测模型在类药物化合物辅助设计中的应用。

Application of high-precision solubility prediction models in the assisted design of drug-like compounds.

作者信息

Gao Yutong

机构信息

School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210029, China.

出版信息

Mol Divers. 2025 May 27. doi: 10.1007/s11030-025-11239-x.

Abstract

Machine learning (ML) techniques are rapidly being applied to drug-assisted design. In order to provide more efficient methods to aid the solubility prediction aspect of drug design, two machine learning models are developed and trained with two distinct feature sets derived from the Zenodo dataset. The machine models are constructed with the multilayer perceptron as the core, combining Bayesian optimization and Monte Carlo methods to improve prediction accuracy. The training process leverages RMSprop to expedite convergence, utilizes Dropout to avert overfitting, and incorporates a Self-Attention mechanism to focus on important features. Based on the three types of compounds, the correlation coefficients all remain above 0.99 compared to the actual solubility. The average absolute errors of the solubility prediction results of the two models are less than 0.200 mol/L and 0.050 mol/L. Both trained models are capable of predicting the solubility of thousands of compounds in just 94.7 ms and 57.7 ms. Using these two models, it is possible to assist with faster and more rational design of drug-like compounds.

摘要

机器学习(ML)技术正迅速应用于药物辅助设计。为了提供更有效的方法来辅助药物设计中的溶解度预测,开发了两个机器学习模型,并使用从Zenodo数据集中提取的两个不同特征集进行训练。这些机器模型以多层感知器为核心构建,结合贝叶斯优化和蒙特卡罗方法以提高预测准确性。训练过程利用RMSprop加速收敛,利用随机失活避免过拟合,并纳入自注意力机制以关注重要特征。基于这三种类型的化合物,与实际溶解度相比,相关系数均保持在0.99以上。两个模型的溶解度预测结果的平均绝对误差分别小于0.200 mol/L和0.050 mol/L。两个经过训练的模型都能够在仅94.7毫秒和57.7毫秒内预测数千种化合物的溶解度。使用这两个模型,可以辅助更快、更合理地设计类药物化合物。

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