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通过消息传递对大分子的分析电子密度进行机器学习。

Machine Learning of Analytical Electron Density in Large Molecules Through Message-Passing.

机构信息

Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain.

Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agraria, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain.

出版信息

J Chem Inf Model. 2021 Jun 28;61(6):2658-2666. doi: 10.1021/acs.jcim.1c00227. Epub 2021 May 19.

Abstract

Machine learning milestones in computational chemistry are overshadowed by their unaccountability and the overwhelming zoo of tools for each specific task. A promising path to tackle these problems is using machine learning to reproduce physical magnitudes as a basis to derive many other properties. By using a model of the electron density consisting of an analytical expansion on a linear set of isotropic and anisotropic functions, we implemented in this work a message-passing neural network able to reproduce electron density in molecules with just a 2.5% absolute error in complex cases. We also adapted our methodology to describe electron density in large biomolecules (proteins) and to obtain atomic charges, interaction energies, and DFT energies. We show that electron density learning is a new promising avenue with a variety of forthcoming applications.

摘要

计算化学中的机器学习里程碑被其不可解释性和针对每个特定任务的大量工具所掩盖。解决这些问题的一个有前途的途径是使用机器学习来复制物理量,以此为基础来推导出许多其他的性质。通过使用一个由线性各向同性和各向异性函数组成的解析展开的电子密度模型,我们在这项工作中实现了一个消息传递神经网络,它能够在复杂情况下将分子的电子密度精确到 2.5%以内。我们还调整了我们的方法来描述大分子(蛋白质)中的电子密度,并获得原子电荷、相互作用能和 DFT 能量。我们表明,电子密度学习是一个具有多种潜在应用的新的有前途的途径。

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