Tao Y - Search Results

1

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.

Zeng J, Tao Y, Giese TJ, York DM. Zeng J, et al. Among authors: tao y. J Chem Phys. 2023 Mar 28;158(12):124110. doi: 10.1063/5.0139281. J Chem Phys. 2023. PMID: 37003741 Free PMC article.

2

Validation of Free Energy Methods in AMBER.

Tsai HC, Tao Y, Lee TS, Merz KM Jr, York DM. Tsai HC, et al. Among authors: tao y. J Chem Inf Model. 2020 Nov 23;60(11):5296-5300. doi: 10.1021/acs.jcim.0c00285. Epub 2020 Jul 6. J Chem Inf Model. 2020. PMID: 32551593 Free PMC article.

3

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.

Lee TS, Lin Z, Allen BK, Lin C, Radak BK, Tao Y, Tsai HC, Sherman W, York DM. Lee TS, et al. Among authors: tao y. J Chem Theory Comput. 2020 Sep 8;16(9):5512-5525. doi: 10.1021/acs.jctc.0c00237. Epub 2020 Aug 12. J Chem Theory Comput. 2020. PMID: 32672455 Free PMC article.

4

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Lee TS, Allen BK, Giese TJ, Guo Z, Li P, Lin C, McGee TD Jr, Pearlman DA, Radak BK, Tao Y, Tsai HC, Xu H, Sherman W, York DM. Lee TS, et al. Among authors: tao y. J Chem Inf Model. 2020 Nov 23;60(11):5595-5623. doi: 10.1021/acs.jcim.0c00613. Epub 2020 Sep 16. J Chem Inf Model. 2020. PMID: 32936637 Free PMC article.

5

QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery.

Zeng J, Tao Y, Giese TJ, York DM. Zeng J, et al. Among authors: tao y. J Chem Theory Comput. 2023 Feb 28;19(4):1261-1275. doi: 10.1021/acs.jctc.2c01172. Epub 2023 Jan 25. J Chem Theory Comput. 2023. PMID: 36696673 Free PMC article.

6

Surface-Accelerated String Method for Locating Minimum Free Energy Paths.

Giese TJ, Ekesan Ş, McCarthy E, Tao Y, York DM. Giese TJ, et al. Among authors: tao y. J Chem Theory Comput. 2024 Mar 12;20(5):2058-2073. doi: 10.1021/acs.jctc.3c01401. Epub 2024 Feb 17. J Chem Theory Comput. 2024. PMID: 38367218 Free PMC article.

7

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.

Tao Y, Giese TJ, Ekesan Ş, Zeng J, Aradi B, Hourahine B, Aktulga HM, Götz AW, Merz KM Jr, York DM. Tao Y, et al. J Chem Phys. 2024 Jun 14;160(22):224104. doi: 10.1063/5.0211276. J Chem Phys. 2024. PMID: 38856060

8

Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.

Tao Y, Giese TJ, York DM. Tao Y, et al. Molecules. 2024 Jun 6;29(11):2703. doi: 10.3390/molecules29112703. Molecules. 2024. PMID: 38893576 Free PMC article.

9

Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.

Giese TJ, Zeng J, Lerew L, McCarthy E, Tao Y, Ekesan Ş, York DM. Giese TJ, et al. Among authors: tao y. J Phys Chem B. 2024 Jul 4;128(26):6257-6271. doi: 10.1021/acs.jpcb.4c01466. Epub 2024 Jun 21. J Phys Chem B. 2024. PMID: 38905451 Free PMC article.

10

We Are All Stars-Collaboration Builds Constellations and Galaxies.

Tao Y. Tao Y. ACS Environ Au. 2023 Sep 20;3(5):249. doi: 10.1021/acsenvironau.3c00042. eCollection 2023 Sep 20. ACS Environ Au. 2023. PMID: 37743949 Free PMC article. No abstract available.

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