Huang Lab - Publication

Journal Articles

28. Shen, M.; Huang, Y.;Cai, Z.; Cherny, V. V.; DeCoursey, T. E.; Shen, J.

Interior pH Sensing Residue of Human Voltage-Gated Proton Channel Hv1 is Histidine 168

Biophysical Journal,123,1-10(2024)

27. Cai, Z.#; Peng, H.#; Sun, S.#; He, J.; Luo, F.; Huang, Y.*

DeepKa Web Server: High-Throughput Protein pKa Prediction

Journal of Chemical Information and Modeling,64,2933-2940(2024)

26. Hwang, W.*; ...; Huang, Y.; ...; Shen, J.; ....; Karplus M. (Nobel Prize Chemistry 2013)

CHARMM at 45: Enhancements in accessibility, functionality, and speed

The Journal of Physical Chemistry B,In Press,(2024)

25. Luo, F.; Cai, Z.; Huang, Y.*

Progress in protein pKa prediction

Acta Physica Sinica,72,248704(2023)

24. Cai, Z.; Liu, T.; He, J.; Lei, X.; Luo, F.; Huang, Y.*

Basis for accurate protein pKa prediction with machine learning

Journal of Chemical Information and Modeling,63,2936-2947(2023)

23. Henderson, J. A.;Liu, R.;Harris, J. A.; Huang, Y.;Oliveira, V. M.;Shen, J*

A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]

Living Journal of Computional Molecular Science,4,1563(2022)

22. Huang, Y.; Henderson, J. A.; Shen, J.*

Continuous constant pH molecular dynamics simulations of transmembrane proteins

Methods Mol. Biol.,2302,275-287(2021)

21. Cai, Z.#; Luo, F.#; Wang, Y.; Li, E.; Huang, Y.*（代表作）

Protein pKa prediction with machine learning

ACS Omega,6,34823-34831(2021)

20. Lyu, Z.#; Wang, Z.#; Luo, F.; Shuai, J.; Huang, Y.

Protein secondary structure prediction with a reductive deep learning method

Frontiers of Bioengineering and Biotechnology,9,687426(2021)

19. Huang, Y.; Qu, J.; Li, X.; Zhong J.; Wu, Y.; Cai M.; Gao, X.; Pearson, J. E.; Shuai, J.

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

Physical Review E,101,012418(2020)

18. Henderson, J. A.; Huang, Y.; Beckstein O.; Shen, J.*

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

Proceedings of the National Academy of Sciences of USA,117,25517-25522(2020)

17. Case, D.A.; Ben-Shalom, I.Y.; Brozell, S.R.; Cerutti, D.S. Cheatham, III, T.E.; Cruzeiro, V.W.D.; Darden, T.A.; Duke, R.E.; Ghoreishi, D.; Giambasu, G.; Gilson, M.K.; Gohlke, H.; Goetz, A.W.; Greene, D.; Harris, R.; Homeyer, N.; Huang, Y. ; et al.

AMBER 2019

University of California, San Francisco,MD package,1-960(2019)

16. Li, Z.; Zhang, X.; Wang, Q.;Li, C.; Zhang, N.; Zhang, X.; Xu, B.; Ma, B.; Schrader, T.; Coates, L.; Kovalevsky, A.; Huang, Y.; Wan, Q.

Understanding the pH-dependent reaction mechanism of a glycoside hydrolase using high resolution X-ray and neutron crystallography.

ACS Catalysis,8,8058-8069(2018)

15. Case, D.A.; Ben-Shalom, I.Y.; Brozell, S.R.; Cerutti, D.S. Cheatham, III, T.E.; Cruzeiro, V.W.D.; Darden, T.A.; Duke, R.E.; Ghoreishi, D.; Giambasu, G.; Gilson, M.K.; Gohlke, H.; Goetz, A.W.; Greene, D.; Harris, R.; Homeyer, N.; Huang, Y. ; et al.

Amber 2018

University of California, San Francisco ,MD package,1-927(2018)

14. Huang, Y.; Harris, R. C.; Shen, J.*

Generalized Born based continuous constant pH molecular dynamics in Amber: Implementation, benchmarking and analysis.

Journal of Chemical Information and Modeling,58,1372-1383(2018)

13. Huang, Y.; Yue, Z.; Tsai, C. C.; Henderson, J. A.; Shen, J.*

Predicting catalytic proton donors and nucleophiles in enzymes: how adding dynamics help elucidate the structure-function relationships.

The Journal of Physical Chemistry Letters,9,1179-1184(2018)

12. Ling, A.; Huang, Y.; Shuai, J.; Lan, Y.*

Channel based generating function approach to the stochastic Hodgkin-Huxley neuronal system.

Scientific Reports,6,22662(2016)

11. Chen, W.; Huang, Y.; Shen, J.*

Conformational activation of a transmembrane proton channel from constant pH molecular dynamics.

The Journal of Physical Chemistry Letters,7,3961-3966(2016)

10. Huang, Y.; Chen, W.; Wallace, J. A.; Shen, J.* (代表作)

All-atom continuous constant pH molecular dynamics with particle mesh Ewald and titratable water.

Journal of Chemical Theory and Computation,12,5411-5421(2016)

9. Huang, Y.; Chen, W.; Dotson, D. L.; Beckstein, O.; Shen, J.* (代表作)

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA.

Nature Communications,7,12940(2016)

8. Huang, Y.; Li, X.; Shuai, J.*

Langevin approach with scaled noise for stochastic channel dynamics in Hodgkin-Huxley neuron.

Chinese Physics B,24,120501(2015)

7. Huang, Y.; Rudiger, S.; Shuai, J.

Accurate Langevin approaches to simulate Markovian channel dynamics.

Physical Biology,12,061001(2015)

6. Qi, H.; Huang, Y.; Rudiger, S.; Shuai, J.*

Frequency and relative prevalence of calcium blips and puffs transition in a model of small IP3R clusters.

Biophysical Journal,106,2553-2363(2014)

5. Huang, Y.; Rudiger, S.; Shuai, J.* (代表作)

Channel-based Langevin approach for the stochastic Hodgkin-Huxley neuron.

Physical Review E,87,012716(2013)

4. Huang, Y.; Rudiger, S.; Shuai, J.*

Langevin approach for stochastic Hodgkin-Huxley dynamics with discretization of channel open fraction.

Physics Letters A,337,3223-3227(2013)

3. Huang, Y.; Shuai, J.* (代表作)

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

The Journal of Physical Chemistry B,117,6138-6148(2013)

2. Huang, Y.; Rudiger, S.; Shuai, J.*

Modified langevin approach for a stochastic calcium puff model.

European Physics Journal B,83,401(2011)

1. Shuai, J.*; Huang, Y.; Rudiger, S.

Puff-wave transition in an inhomogeneous model for calcium signals.

Physical Review E,81,041904(2010)