Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials
Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials
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DOI：
10.1021/acs.jcim.2c00817
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发表时间：
2022-09-16
影响因子：
5.6
通讯作者：
Isayev, Olexandr
中科院分区：
文献类型：
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作者：
Liu, Zhen;Zubatiuk, Tetiana;Isayev, Olexandr
计算程序加速了化学发现过程，但通常需要适当的三维分子信息作为输入的一部分。获得最佳的分子结构是具有挑战性的，因为它需要枚举和优化的立体异构体和构象异构体的巨大空间。我们开发了基于Python的Auto 3D包，用于使用SMILES作为输入生成低能量3D结构。Auto 3D基于最先进的算法，可以自动化异构体枚举和重复过滤过程，3D构建过程，几何优化和排名过程。在50个具有多个未指定立体中心的分子上进行测试，Auto 3D是多个未指定的保证，可以找到产生最低能量构象的立体构型。借助Auto 3D，我们提供了ANI模型的扩展。新模型被称为ANI-2xt，是在一个富含互变异构体的数据集上训练的。ANI-2xt的基准与DFT方法的几何优化和电子和吉布斯自由能计算。与ANI-2x相比，ANI-2xt在以金标准耦合簇计算为参考的互变异构反应能量计算中，误差减少了42%。ANI-2xt能准确地预测能量，比DFT方法快几个数量级。
Computational programs accelerate the chemical discovery processes but often need proper three-dimensional molecular information as part of the input. Getting optimal molecular structures is challenging because it requires enumerating and optimizing a huge space of stereoisomers and conformers. We developed the Python-based Auto3D package for generating the low-energy 3D structures using SMILES as the input. Auto3D is based on state-of-the-art algorithms and can automatize the isomer enumeration and duplicate filtering process, 3D building process, geometry optimization, and ranking process. Tested on 50 molecules with multiple unspecified stereocenters, Auto3D is multiple unspecified guaranteed to find the stereoconfiguration that yields the lowest-energy conformer. With Auto3D, we provide an extension of the ANI model. The new model, dubbed ANI-2xt, is trained on a tautomer-rich data set. ANI-2xt is benchmarked with DFT methods on geometry optimization and electronic and Gibbs free energy calculations. Compared with ANI-2x, ANI-2xt provides a 42% error reduction for tautomeric reaction energy calculations when using the gold-standard coupled-cluster calculation as the reference. ANI-2xt can accurately predict the energies and is several orders of magnitude faster than DFT methods.