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将 ANI 深度学习分子势的适用性扩展到硫和卤素。

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens.

机构信息

Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.

Center for Non-Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.

出版信息

J Chem Theory Comput. 2020 Jul 14;16(7):4192-4202. doi: 10.1021/acs.jctc.0c00121. Epub 2020 Jun 29.

DOI:10.1021/acs.jctc.0c00121
PMID:32543858
Abstract

Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here, we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, and S) make up ∼90% of drug-like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and nonbonded interactions. ANI-2x is shown to accurately predict molecular energies compared to density functional theory with a ∼10 factor speedup and a negligible slowdown compared to ANI-1x and shows subchemical accuracy across most of the COMP6 benchmark. The resulting model is a valuable tool for drug development which can potentially replace both quantum calculations and classical force fields for a myriad of applications.

摘要

机器学习 (ML) 方法已成为广泛应用领域(如人脸识别和自动驾驶)中的强大预测工具。在科学领域,计算化学家与物理学家一直将 ML 用于预测物理现象,例如原子势能面和反应途径。为了准确模拟含有 H、C、N 和 O 等化学元素的有机分子,人们已经开发出了可转移的 ML 势能,如 ANI-1x。在这里,我们提供了 ANI-1x 模型的扩展。新模型称为 ANI-2x,经过训练可以预测另外三种化学元素:S、F 和 Cl。此外,ANI-2x 还进行了扭转细化训练,以更好地预测分子扭转轮廓。这些新特性为有机化学和药物开发领域开辟了广泛的新应用。这七种元素(H、C、N、O、F、Cl 和 S)占类似药物分子的 90%左右。为了表明这些添加不会牺牲准确性,我们已经在一系列有机分子和应用中测试了这个模型,包括 COMP6 基准测试、二面角旋转、构象评分和非键相互作用。与密度泛函理论相比,ANI-2x 能够准确预测分子能量,速度提高了约 10 倍,与 ANI-1x 相比几乎没有减速,并且在大多数 COMP6 基准测试中都具有亚化学精度。该模型是药物开发的一个有价值的工具,它可以替代量子计算和经典力场,应用于无数的领域。

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