Shao Y - Search Results

1

Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation.

Van R, Pan X, Rostami S, Liu J, Agarwal PK, Brooks B, Rajan R, Shao Y. Van R, et al. Among authors: shao y. Biochemistry. 2024 Dec 16. doi: 10.1021/acs.biochem.4c00651. Online ahead of print. Biochemistry. 2024. PMID: 39680038

2

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions.

Pan X, Yang J, Van R, Epifanovsky E, Ho J, Huang J, Pu J, Mei Y, Nam K, Shao Y. Pan X, et al. Among authors: shao y. J Chem Theory Comput. 2021 Sep 14;17(9):5745-5758. doi: 10.1021/acs.jctc.1c00565. Epub 2021 Sep 1. J Chem Theory Comput. 2021. PMID: 34468138 Free PMC article.

3

Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian.

Pan X, Van R, Epifanovsky E, Liu J, Pu J, Nam K, Shao Y. Pan X, et al. Among authors: shao y. J Phys Chem B. 2022 Jun 2:10.1021/acs.jpcb.2c02262. doi: 10.1021/acs.jpcb.2c02262. Online ahead of print. J Phys Chem B. 2022. PMID: 35653199 Free PMC article.

4

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions.

Pan X, Van R, Pu J, Nam K, Mao Y, Shao Y. Pan X, et al. Among authors: shao y. J Chem Theory Comput. 2023 Nov 28;19(22):8234-8244. doi: 10.1021/acs.jctc.3c00973. Epub 2023 Nov 9. J Chem Theory Comput. 2023. PMID: 37943896 Free PMC article.

5

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation.

Li P, Jia X, Pan X, Shao Y, Mei Y. Li P, et al. Among authors: shao y. J Chem Theory Comput. 2018 Nov 13;14(11):5583-5596. doi: 10.1021/acs.jctc.8b00571. Epub 2018 Oct 26. J Chem Theory Comput. 2018. PMID: 30336015

6

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching.

Pan X, Li P, Ho J, Pu J, Mei Y, Shao Y. Pan X, et al. Among authors: shao y. Phys Chem Chem Phys. 2019 Oct 7;21(37):20595-20605. doi: 10.1039/c9cp02593f. Epub 2019 Sep 11. Phys Chem Chem Phys. 2019. PMID: 31508625 Free PMC article.

7

Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation.

Snyder R, Kim B, Pan X, Shao Y, Pu J. Snyder R, et al. Among authors: shao y. J Chem Phys. 2023 Aug 7;159(5):054107. doi: 10.1063/5.0156327. J Chem Phys. 2023. PMID: 37530109 Free PMC article.

8

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

Jia X, Wang M, Shao Y, König G, Brooks BR, Zhang JZ, Mei Y. Jia X, et al. Among authors: shao y. J Chem Theory Comput. 2016 Feb 9;12(2):499-511. doi: 10.1021/acs.jctc.5b00920. Epub 2016 Jan 12. J Chem Theory Comput. 2016. PMID: 26731197

9

Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations.

Snyder R, Kim B, Pan X, Shao Y, Pu J. Snyder R, et al. Among authors: shao y. Phys Chem Chem Phys. 2022 Oct 27;24(41):25134-25143. doi: 10.1039/d2cp02820d. Phys Chem Chem Phys. 2022. PMID: 36222412 Free PMC article.

10

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

Wang M, Li P, Jia X, Liu W, Shao Y, Hu W, Zheng J, Brooks BR, Mei Y. Wang M, et al. Among authors: shao y. J Chem Inf Model. 2017 Oct 23;57(10):2476-2489. doi: 10.1021/acs.jcim.7b00001. Epub 2017 Oct 2. J Chem Inf Model. 2017. PMID: 28933850

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