Xuhui Huang

HKUST Profile Google Scholar Scopus Author ID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 64

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

The Journal of chemical physics

Journal of the American Chemical Society

Journal of chemical theory and computation

Hong Kong University of Science and Technology

Columbia University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Hong Kong University of Science and Technology Jul 01 2019

Hong Kong

Professor :: Department of Chemistry, Department of Chemical and Biological Engineering

The Hong Kong University of Science and Technology - Jun 30 2019

Hong Kong

Padma Harilela Associate Professor of Science :: Chemistry

Hong Kong University of Science and Technology Jan 01 2015 - Jun 30 2019

Hong Kong

Associate Profrssor :: Department of Chemistry, Department of Chemical and Biological Engineering

Hong Kong University of Science and Technology Jan 10 2010 - Dec 31 2014

Hong Kong

Assistant Professor :: Department of Chemistry

Stanford University Sep 01 2008 - Dec 31 2009

United States

Research Associate :: Department of Bioengineering

Stanford University Aug 01 2006 - Sep 01 2008

United States

Simbios Distinguished Postdoctoral Fellow :: Department of Bioengineering

Education History

Columbia University Sep 01 2001 - Jul 31 2006

United States

PHD :: Chemistry Department

University of Science and Technology of China Sep 01 1997 - Jul 01 2001

China

BSC :: Department of Chemical Physics

Publications

Yue Wu, Siqin Cao, Yunrui Qiu, Xuhui Huang
Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes. The Journal of chemical physics 160 (12) (2024)
Ilona C Unarta, Siqin Cao, Eshani C Goonetilleke, Jiani Niu, Samuel H Gellman, Xuhui Huang
Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. The journal of physical chemistry. B 128 (10) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Yue Wu, Siqin Cao, Yunrui Qiu, Xuhui Huang
Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes. The Journal of chemical physics 160 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Ilona C Unarta, Siqin Cao, Eshani C Goonetilleke, Jiani Niu, Samuel H Gellman, Xuhui Huang
Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. The journal of physical chemistry. B 128 (10) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation (2024)
Ilona C Unarta, Siqin Cao, Eshani C Goonetilleke, Jiani Niu, Samuel H Gellman, Xuhui Huang
Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. The journal of physical chemistry. B (2024)
Ilona C Unarta, Siqin Cao, Eshani C Goonetilleke, Jiani Niu, Samuel H Gellman, Xuhui Huang
Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. The journal of physical chemistry. B 128 (10) (2024)
Yue Wu, Siqin Cao, Yunrui Qiu, Xuhui Huang
Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes. The Journal of chemical physics 160 (12) (2024)
Ilona C Unarta, Siqin Cao, Eshani C Goonetilleke, Jiani Niu, Samuel H Gellman, Xuhui Huang
Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. The journal of physical chemistry. B 128 (10) (2024)
Eric M Kohn, Kirill Konovalov, Christian A Gomez, Gillian N Hoover, Andrew Kai-Hei Yik, Xuhui Huang, Jeffrey D Martell
Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS chemical biology (2023)
Anthony J Dominic, Siqin Cao, Andrés Montoya-Castillo, Xuhui Huang
Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently. Journal of the American Chemical Society 145 (18) (2023)
Anthony J Dominic, Siqin Cao, Andrés Montoya-Castillo, Xuhui Huang
Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently. Journal of the American Chemical Society 145 (18) (2023)
Yunrui Qiu, Michael S O'Connor, Mingyi Xue, Bojun Liu, Xuhui Huang
An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes. Journal of chemical theory and computation (2023)
Anthony J Dominic, Thomas Sayer, Siqin Cao, Thomas E Markland, Xuhui Huang, Andrés Montoya-Castillo
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (12) (2023)
Kirill A Konovalov, Cheng-Guo Wu, Yunrui Qiu, Vijaya Kumar Balakrishnan, Pankaj Singh Parihar, Michael S O'Connor, Yongna Xing, Xuhui Huang
Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A. The Journal of chemical physics 158 (21) (2023)
Cheng-Guo Wu, Vijaya K Balakrishnan, Ronald A Merrill, Pankaj Singh Parihar, Kirill Konovolov, Yu-Chia Chen, Zhen Xu, Hui Wei, Ramya Sundaresan, Qiang Cui, Brian E Wadzinski, Mark R Swingle, Alla Musiyenko, Wendy K Chung, Richard E Honkanen, Aussie Suzuki, Xuhui Huang, Stefan Strack, Yongna Xing
B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proceedings of the National Academy of Sciences of the United States of America 121 (1) (2023)
Anthony J Dominic, Siqin Cao, Andrés Montoya-Castillo, Xuhui Huang
Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently. Journal of the American Chemical Society (2023)
Cheng-Guo Wu, Vijaya K Balakrishnan, Ronald A Merrill, Pankaj Singh Parihar, Kirill Konovolov, Yu-Chia Chen, Zhen Xu, Hui Wei, Ramya Sundaresan, Qiang Cui, Brian E Wadzinski, Mark R Swingle, Alla Musiyenko, Wendy K Chung, Richard E Honkanen, Aussie Suzuki, Xuhui Huang, Stefan Strack, Yongna Xing
B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proceedings of the National Academy of Sciences of the United States of America 121 (1) (2023)
Cheng-Guo Wu, Vijaya K Balakrishnan, Ronald A Merrill, Pankaj Singh Parihar, Kirill Konovolov, Yu-Chia Chen, Zhen Xu, Hui Wei, Ramya Sundaresan, Qiang Cui, Brian E Wadzinski, Mark R Swingle, Alla Musiyenko, Wendy K Chung, Richard E Honkanen, Aussie Suzuki, Xuhui Huang, Stefan Strack, Yongna Xing
B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proceedings of the National Academy of Sciences of the United States of America 121 (1) (2023)
Siqin Cao, Yunrui Qiu, Michael L Kalin, Xuhui Huang
Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels. The Journal of chemical physics 159 (13) (2023)
Cheng-Guo Wu, Vijaya K Balakrishnan, Ronald A Merrill, Pankaj Singh Parihar, Kirill Konovolov, Yu-Chia Chen, Zhen Xu, Hui Wei, Ramya Sundaresan, Qiang Cui, Brian E Wadzinski, Mark R Swingle, Alla Musiyenko, Wendy K Chung, Richard E Honkanen, Aussie Suzuki, Xuhui Huang, Stefan Strack, Yongna Xing
B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proceedings of the National Academy of Sciences of the United States of America 121 (1) (2023)
Anthony J Dominic, Siqin Cao, Andrés Montoya-Castillo, Xuhui Huang
Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently. Journal of the American Chemical Society 145 (18) (2023)
Mario A Cribari, Maxwell J Unger, Ilona C Unarta, Ashley N Ogorek, Xuhui Huang, Jeffrey D Martell
Ultrahigh-Throughput Directed Evolution of Polymer-Degrading Enzymes Using Yeast Display. Journal of the American Chemical Society (2023)
Cheng-Guo Wu, Vijaya K Balakrishnan, Ronald A Merrill, Pankaj Singh Parihar, Kirill Konovolov, Yu-Chia Chen, Zhen Xu, Hui Wei, Ramya Sundaresan, Qiang Cui, Brian E Wadzinski, Mark R Swingle, Alla Musiyenko, Wendy K Chung, Richard E Honkanen, Aussie Suzuki, Xuhui Huang, Stefan Strack, Yongna Xing
B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proceedings of the National Academy of Sciences of the United States of America 121 (1) (2023)
Anthony J Dominic, Thomas Sayer, Siqin Cao, Thomas E Markland, Xuhui Huang, Andrés Montoya-Castillo
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (12) (2023)
Anthony J Dominic, Thomas Sayer, Siqin Cao, Thomas E Markland, Xuhui Huang, Andrés Montoya-Castillo
Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations. Proceedings of the National Academy of Sciences of the United States of America 120 (12) (2023)
Siqin Cao, Michael L Kalin, Xuhui Huang
EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. Journal of computational chemistry (2023)
Siqin Cao, Yunrui Qiu, Ilona C Unarta, Eshani C Goonetilleke, Xuhui Huang
The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules. The journal of physical chemistry. B 126 (43) (2022)
Hanlin Gu, Wei Wang, Siqin Cao, Ilona Christy Unarta, Yuan Yao, Fu Kit Sheong, Xuhui Huang
RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics. Physical chemistry chemical physics : PCCP 24 (3) (2022)
Xiao-Yan Zheng, Michael Ho-Yeung Chan, Alan Kwun-Wa Chan, Siqin Cao, Maggie Ng, Fu Kit Sheong, Chu Li, Eshani Chrisana Goonetilleke, William Wai Yan Lam, Tai-Chu Lau, Xuhui Huang, Vivian Wing-Wah Yam
Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes. Proceedings of the National Academy of Sciences of the United States of America 119 (12) (2022)
Ilona Christy Unarta, Jianchao Xu, Yuan Shang, Carina Hey Pui Cheung, Ruichi Zhu, Xudong Chen, Siqin Cao, Peter Pak-Hang Cheung, Donald Bierer, Mingjie Zhang, Xuhui Huang, Xuechen Li
Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain. RSC chemical biology 2 (4) (2021)
Xinzhou Xu, Lu Zhang, Julie Tung Sem Chu, Yuqing Wang, Alex Wing Hong Chin, Tin Hang Chong, Zixi Dai, Leo Lit Man Poon, Peter Pak-Hang Cheung, Xuhui Huang
A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic acids research 49 (15) (2021)
Juntaek Oh, Ji Shin, Ilona Christy Unarta, Wei Wang, Aaron W Feldman, Rebekah J Karadeema, Liang Xu, Jun Xu, Jenny Chong, Ramanarayanan Krishnamurthy, Xuhui Huang, Floyd E Romesberg, Dong Wang
Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nature chemical biology 17 (8) (2021)
Kirill A Konovalov, Ilona Christy Unarta, Siqin Cao, Eshani C Goonetilleke, Xuhui Huang
Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning. JACS Au 1 (9) (2021)
Chu Li, Zhuo Liu, Eshani C Goonetilleke, Xuhui Huang
Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation. Nature communications 12 (1) (2021)
Ilona Christy Unarta, Siqin Cao, Shintaroh Kubo, Wei Wang, Peter Pak-Hang Cheung, Xin Gao, Shoji Takada, Xuhui Huang
Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model. Proceedings of the National Academy of Sciences of the United States of America 118 (17) (2021)
Taylor R Quinn, C Nicklaus Steussy, Brandon E Haines, Jinping Lei, Wei Wang, Fu Kit Sheong, Cynthia V Stauffacher, Xuhui Huang, Per-Ola Norrby, Paul Helquist, Olaf G Wiest
Microsecond timescale MD simulations at the transition state of PmHMGR predict remote allosteric residues. Chemical science 12 (18) (2021)
Carina Hey Pui Cheung, Jianchao Xu, Chi Lung Lee, Yanfeng Zhang, Ruohan Wei, Donald Bierer, Xuhui Huang, Xuechen Li
Construction of diverse peptide structural architectures via chemoselective peptide ligation. Chemical science 12 (20) (2021)
Lizhe Zhu, Hanlun Jiang, Siqin Cao, Ilona Christy Unarta, Xin Gao, Xuhui Huang
Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex. Communications biology 4 (1) (2021)
Siqin Cao, Andrés Montoya-Castillo, Wei Wang, Thomas E Markland, Xuhui Huang
On the advantages of exploiting memory in Markov state models for biomolecular dynamics. The Journal of chemical physics 153 (1) (2021)
Congmin Yuan, Eshani C Goonetilleke, Ilona Christy Unarta, Xuhui Huang
Incorporation efficiency and inhibition mechanism of 2'-substituted nucleotide analogs against SARS-CoV-2 RNA-dependent RNA polymerase. Physical chemistry chemical physics : PCCP 23 (36) (2021)
Cong Pan, Chengwen Liu, Junhui Peng, Pengyu Ren, Xuhui Huang
Three-site and five-site fixed-charge water models compatible with AMOEBA force field. Journal of computational chemistry 41 (10) (2020)
Sijia Peng, Xiaowei Wang, Lu Zhang, Shanshan He, Xin Sheng Zhao, Xuhui Huang, Chunlai Chen
Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models. Proceedings of the National Academy of Sciences of the United States of America 117 (36) (2020)
Kirill A Konovalov, Fátima Pardo-Avila, Carmen Ka Man Tse, Juntaek Oh, Dong Wang, Xuhui Huang
8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II. The Journal of biological chemistry 294 (13) (2019)
Kirill A Konovalov, Wei Wang, Xuhui Huang
Conformational selection turns on phenylalanine hydroxylase. The Journal of biological chemistry 293 (51) (2019)
Yujie Tu, Yeqing Yu, Zhibiao Zhou, Sheng Xie, Bicheng Yao, Shujuan Guan, Bo Situ, Yong Liu, Ryan Tsz Kin Kwok, Jacky W Y Lam, Sijie Chen, Xuhui Huang, Zebing Zeng, Ben-Zhong Tang
Specific and Quantitative Detection of Albumin in Biological Fluids by Tetrazolate-Functionalized Water-Soluble AIEgens. ACS applied materials & interfaces 11 (33) (2019)
Jordy Homing Lam, Yu Li, Lizhe Zhu, Ramzan Umarov, Hanlun Jiang, Amélie Héliou, Fu Kit Sheong, Tianyun Liu, Yongkang Long, Yunfei Li, Liang Fang, Russ B Altman, Wei Chen, Xuhui Huang, Xin Gao
A deep learning framework to predict binding preference of RNA constituents on protein surface. Nature communications 10 (1) (2019)
Zheng Zhao, Xiao-Yan Zheng, Lili Du, Yu Xiong, Wei He, Xiuxiu Gao, Chunli Li, Yingjie Liu, Bin Xu, Jing Zhang, Fengyan Song, Ying Yu, Xueqian Zhao, Yuanjing Cai, Xuewen He, Ryan T K Kwok, Jacky W Y Lam, Xuhui Huang, David Lee Phillips, Hua Wang, Ben-Zhong Tang
Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process. Nature communications 10 (1) (2019)
Lizhe Zhu, Fu Kit Sheong, Siqin Cao, Song Liu, Ilona C Unarta, Xuhui Huang
TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules. The Journal of chemical physics 150 (12) (2019)
Wei Wang, Tong Liang, Fu Kit Sheong, Xiaodan Fan, Xuhui Huang
An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling. The Journal of chemical physics 149 (7) (2018)
Yu Zhou, Chen Li, Jianzhao Peng, Liangxu Xie, Ling Meng, Qingrong Li, Jianfu Zhang, Xiang David Li, Xin Li, Xuhui Huang, Xiaoyu Li
DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery. Journal of the American Chemical Society 140 (46) (2018)
Jinping Lei, Gang Sheng, Peter Pak-Hang Cheung, Shenglong Wang, Yu Li, Xin Gao, Yingkai Zhang, Yanli Wang, Xuhui Huang
Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proceedings of the National Academy of Sciences of the United States of America 116 (3) (2018)
Luming Meng, Fu Kit Sheong, Xiangze Zeng, Lizhe Zhu, Xuhui Huang
Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems. The Journal of chemical physics 147 (4) (2018)
Haoke Zhang, Xiaoyan Zheng, Ni Xie, Zikai He, Junkai Liu, Nelson L C Leung, Yingli Niu, Xuhui Huang, Kam Sing Wong, Ryan Tsz Kin Kwok, Herman H Y Sung, Ian D Williams, Anjun Qin, Jacky W Y Lam, Ben-Zhong Tang
Why Do Simple Molecules with "Isolated" Phenyl Rings Emit Visible Light? Journal of the American Chemical Society 139 (45) (2017)
Xiaoyan Zheng, Lizhe Zhu, Xiangze Zeng, Luming Meng, Lu Zhang, Dong Wang, Xuhui Huang
Kinetics-Controlled Amphiphile Self-Assembly Processes. The journal of physical chemistry letters 8 (8) (2017)
Hui-Qing Peng, Xiaoyan Zheng, Ting Han, Ryan T K Kwok, Jacky W Y Lam, Xuhui Huang, Ben-Zhong Tang
Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers. Journal of the American Chemical Society 139 (29) (2017)
Yuan Tian, Xiangze Zeng, Jingxu Li, Yanhong Jiang, Hui Zhao, Dongyuan Wang, Xuhui Huang, Zigang Li
Achieving enhanced cell penetration of short conformationally constrained peptides through amphiphilicity tuning. Chemical science 8 (11) (2017)
Xuehua Pan, Yunjiao He, Jinping Lei, Xuhui Huang, Yanxiang Zhao
Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis. The Journal of biological chemistry 292 (10) (2017)
Liguo Jiang, Siqin Cao, Peter Pak-Hang Cheung, Xiaoyan Zheng, Chris Wai Tung Leung, Qian Peng, Zhigang Shuai, Ben-Zhong Tang, Shuhuai Yao, Xuhui Huang
Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect. Nature communications 8 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Xuhui Huang