The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens
Open accessAbstract
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, 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 non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~106 factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.
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Cites
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Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules
Gómez-Bombarelli, R., Wei, J. N., Duvenaud, D., Hernández-Lobato, J. M., Sánchez-Lengeling, B., Sheberla, D., Aguilera-Iparraguirre, J., Hirzel, T. D., Adams, R. P., & Aspuru-Guzik, A. (2018) · ACS Central Science · doi:10.1021/acscentsci.7b00572 · Cited by 3,106
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost
Smith, J. S., Isayev, O., & Roitberg, A. E. (2017) · Chemical Science · doi:10.1039/c6sc05720a · Cited by 1,921
Self-citationLess is more: Sampling chemical space with active learning
Smith, J. S., Nebgen, B., Lubbers, N., Isayev, O., & Roitberg, A. E. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5023802 · Cited by 811
Self-citationPrediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error
Faber, F. A., Hutchison, L., Huang, B., Gilmer, J., Schoenholz, S. S., Dahl, G. E., Vinyals, O., Kearnes, S., Riley, P. F., & von Lilienfeld, O. A. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00577 · Cited by 651
Machine learning molecular dynamics for the simulation of infrared spectra
Gastegger, M., Behler, J., & Marquetand, P. (2017) · Chemical Science · doi:10.1039/c7sc02267k · Cited by 556
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Batzner, S., Musaelian, A., Sun, L., Geiger, M., Mailoa, J. P., Kornbluth, M., Molinari, N., Smidt, T. E., & Kozinsky, B. (2022) · Nature Communications · doi:10.1038/s41467-022-29939-5 · Cited by 2,285
The transformational role of GPU computing and deep learning in drug discovery
Pandey, M., Fernandez, M., Gentile, F., Isayev, O., Tropsha, A., Stern, A. C., & Cherkasov, A. (2022) · Nature Machine Intelligence · doi:10.1038/s42256-022-00463-x · Cited by 255
Self-citationA critical overview of computational approaches employed for COVID-19 drug discovery
Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J. L., Merz, K. M., et al. (2021) · Chemical Society Reviews · doi:10.1039/d0cs01065k · Cited by 206
Self-citationBasis for Accurate Protein p K a Prediction with Machine Learning
Cai, Z., Liu, T., Lin, Q., He, J., Lei, X., Luo, F., & Huang, Y. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00254 · Cited by 31
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Metadata
- Authors
- Devereux, C., Smith, J. S., Huddleston, K. K., Barros, K., Zubatyuk, R., Isayev, O., & Roitberg, A. E.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-06-16
- Volume
- 16
- Issue
- 7
- Pages
- 4192-4202
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W3034390843
- Cited by
- 441
- References
- 7
- FWCI
- 16.97
- Type
- journal article
- Language
- en
- Open access
- green
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