Huang Y - Search Results

1

Basis for Accurate Protein pK_a Prediction with Machine Learning.

Cai Z, Liu T, Lin Q, He J, Lei X, Luo F, Huang Y. Cai Z, et al. Among authors: huang y. J Chem Inf Model. 2023 May 22;63(10):2936-2947. doi: 10.1021/acs.jcim.3c00254. Epub 2023 May 5. J Chem Inf Model. 2023. PMID: 37146199

2

Protein Secondary Structure Prediction With a Reductive Deep Learning Method.

Lyu Z, Wang Z, Luo F, Shuai J, Huang Y. Lyu Z, et al. Among authors: huang y. Front Bioeng Biotechnol. 2021 Jun 15;9:687426. doi: 10.3389/fbioe.2021.687426. eCollection 2021. Front Bioeng Biotechnol. 2021. PMID: 34211967 Free PMC article.

3

Protein pK _a Prediction with Machine Learning.

Cai Z, Luo F, Wang Y, Li E, Huang Y. Cai Z, et al. Among authors: huang y. ACS Omega. 2021 Dec 7;6(50):34823-34831. doi: 10.1021/acsomega.1c05440. eCollection 2021 Dec 21. ACS Omega. 2021. PMID: 34963965 Free PMC article.

Here, the CpHMD implemented in the Amber molecular dynamics package has been employed (Huang Y.J. Chem. Inf. Model.2018, 58, 1372-1383). Notably, to avoid discontinuities at the boundary, grid charges are proposed to represent protein electrostatics. ...

Here, the CpHMD implemented in the Amber molecular dynamics package has been employed (Huang Y.J. Chem. Inf. Model.2018, 58, 1 …

4

DeepKa Web Server: High-Throughput Protein pK_a Prediction.

Cai Z, Peng H, Sun S, He J, Luo F, Huang Y. Cai Z, et al. Among authors: huang y. J Chem Inf Model. 2024 Apr 22;64(8):2933-2940. doi: 10.1021/acs.jcim.3c02013. Epub 2024 Mar 26. J Chem Inf Model. 2024. PMID: 38530291

5

Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis.

Huang Y, Harris RC, Shen J. Huang Y, et al. J Chem Inf Model. 2018 Jul 23;58(7):1372-1383. doi: 10.1021/acs.jcim.8b00227. Epub 2018 Jul 11. J Chem Inf Model. 2018. PMID: 29949356 Free PMC article.

6

Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins.

Huang Y, Henderson JA, Shen J. Huang Y, et al. Methods Mol Biol. 2021;2302:275-287. doi: 10.1007/978-1-0716-1394-8_15. Methods Mol Biol. 2021. PMID: 33877633 Free PMC article.

7

Alternative proton-binding site and long-distance coupling in Escherichia coli sodium-proton antiporter NhaA.

Henderson JA, Huang Y, Beckstein O, Shen J. Henderson JA, et al. Among authors: huang y. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25517-25522. doi: 10.1073/pnas.2005467117. Epub 2020 Sep 24. Proc Natl Acad Sci U S A. 2020. PMID: 32973095 Free PMC article.

8

Anti-cross-correlation between the adjacent open and closed durations of Markovian channels.

Huang Y, Qu J, Li X, Wei F, Zhong J, Wu Y, Cai M, Gao X, Pearson JE, Shuai J. Huang Y, et al. Phys Rev E. 2020 Jan;101(1-1):012418. doi: 10.1103/PhysRevE.101.012418. Phys Rev E. 2020. PMID: 32069561

9

Accurate Langevin approaches to simulate Markovian channel dynamics.

Huang Y, Rüdiger S, Shuai J. Huang Y, et al. Phys Biol. 2015 Sep 25;12(6):061001. doi: 10.1088/1478-3975/12/6/061001. Phys Biol. 2015. PMID: 26403205 Review.

10

Induced dipoles incorporated into all-atom Zn protein simulations with multiscale modeling.

Huang YD, Shuai JW. Huang YD, et al. J Phys Chem B. 2013 May 23;117(20):6138-48. doi: 10.1021/jp4021933. Epub 2013 May 10. J Phys Chem B. 2013. PMID: 23631342

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