Yandong Huang
Yandong Huang
Associate professor, Jimei University, Xiamen, China
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All-atom continuous constant pH molecular dynamics with particle-mesh Ewald and titratable water
Y Huang, W Chen, W Jason, J Shen
Journal of chemical theory and computation 12, 5411-5421, 2016
Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA
Y Huang, W Chen, DL Dotson, O Beckstein, J Shen
Nature Communications 7, 12940, 2016
Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics
W Chen, Y Huang, J Shen
Journal of physical chemistry letter 7, 3961-3966, 2016
Generalized Born based continuous constant pH molecular dynamics in Amber: Implementation, benchmarking and analysis
Y Huang, RC Harris, J Shen
Journal of chemical information and modeling 58 (7), 1372-1383, 2018
Predicting catalytic proton donors and nucleophiles in enzymes: How adding dynamics helps elucidate the structure–function relationships
Y Huang, Z Yue, CC Tsai, JA Henderson, J Shen
The journal of physical chemistry letters 9 (6), 1179-1184, 2018
Protein Secondary Structure Prediction With a Reductive Deep Learning Method
Z Lyu, Z Wang, F Luo, J Shuai, Y Huang
Frontiers in Bioengineering and Biotechnology 9, 687426, 2021
Alternative proton-binding site and long-distance coupling in Escherichia coli sodium–proton antiporter NhaA
JA Henderson, Y Huang, O Beckstein, J Shen
Proceedings of the National Academy of Sciences 117 (41), 25517-25522, 2020
Protein pKa Prediction with Machine Learning
Z Cai, F Luo, Y Wang, E Li, Y Huang
ACS Omega 6, 34823-34831, 2021
Frequency and Relative Prevalence of Calcium Blips and Puffs in a Model of Small IP3R Clusters
H Qi, Y Huang, S Rüdiger, J Shuai
Biophysical Journal 106 (11), 2353-2363, 2014
Channel-based Langevin approach for the stochastic Hodgkin-Huxley neuron
Y Huang, S Rüdiger, J Shuai
Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 87 (1 …, 2013
Understanding the pH-dependent reaction mechanism of a glycoside hydrolase using high-resolution X-ray and neutron crystallography
Z Li, X Zhang, Q Wang, C Li, N Zhang, X Zhang, B Xu, B Ma, TE Schrader, ...
ACS catalysis 8 (9), 8058-8069, 2018
Accurate Langevin approaches to simulate Markovian channel dynamics
Y Huang, S Rüdiger, J Shuai
Physical biology 12 (6), 061001, 2015
Continuous constant pH molecular dynamics simulations of transmembrane proteins
Y Huang, JA Henderson, J Shen
Structure and Function of Membrane Proteins, 275-287, 2021
Puff-wave transition in an inhomogeneous model for calcium signals
J Shuai, Y Huang, S Rüdiger
Physical Review E 81 (4), 041904, 2010
A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]
JA Henderson, R Liu, JA Harris, Y Huang, VM Oliveira, J Shen
Living Journal of Computational Molecular Science 4 (1), 1-24, 2022
Modified Langevin approach for a stochastic calcium puff model
Y Huang, S Rüdiger, J Shuai
The European Physical Journal B 83 (3), 401-407, 2011
Amber 2019
D Case, I Ben-Shalom, S Brozell, D Cerutti, T Cheatham, V Cruzeiro III, ...
University of California, San Francisco, 2019
Langevin approach for stochastic Hodgkin–Huxley dynamics with discretization of channel open fraction
Y Huang, S Rüdiger, J Shuai
Physics Letters A 377 (44), 3223-3227, 2013
Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling
Y Huang, J Shuai
The Journal of Physical Chemistry B 117 (20), 6138-6148, 2013
Basis for Accurate Protein pKa Prediction with Machine Learning
Z Cai, T Liu, Q Lin, J He, X Lei, F Luo, Y Huang
Journal of Chemical Information and Modeling 63 (10), 2936-2947, 2023
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