Personal information

Biophysics, Computational biology, Computational chemistry, Statistical mechanics, Structural biology
United States

Biography

Prof. Huang is currently the Hirschfelder Chair in Theoretical Chemistry in Department of Chemistry at University of Wisconsin-Madison (UW-Madison), and he also serves as Director of Theoretical Chemistry Institute at UW-Madison. He obtained his Ph.D. degree from Columbia University in 2006 with Prof. Bruce Berne. He did his postdoc research at Stanford University with Profs. Michael Levitt (Nobel Laureate in Chemistry) and Vijay Pande, He joined Hong Kong University of Scientific and Technology (HKUST) as an assistant professor in 2010, and received an early promotion to the tenured Associated Professor at Jan 2015. Between 2017 and 2019, he was the Padma Harilela Associate Professor of Science at HKUST. Between July 2019 and Aug 2021, he was the full professor at Department of Chemistry and Department of Chemical and Biological Engineering at HKUST. He Joined Department of Chemistry at UW-Madison from Sept 2021. His research is focused on developing and applying statistical mechanics based algorithms to model functional conformational changes of complex biological systems. He has published over 100 papers in top journals including Science, Nature, PNAS, and JACS. Prof. Huang has also received a series of awards including the American Chemical Society OpenEye Outstanding Junior Faculty Award (2014); School Research Award, HKUST School of Science (2013), and Hong Kong Research Grant Council Early Career Award (2013); American Chemical Society CCG Excellence Award (2006); and Pople Medal by Asia-Pacific Association of Theoretical and Computational Chemists (2021). He was elected as a founding member of Young Academy of Sciences of Hong Kong, and serves as its Vice President between 2018 and 2021.

Activities

Employment (7)

University of Wisconsin–Madison: Madison, Wisconsin, US

2021-09 to present | Hirschfelder Chair Professor in Theoretical Chemistry (Chemistry)
Employment
Source: Self-asserted source
Huang, Xuhui

Hong Kong University of Science and Technology: Kowloon, HK

2019-07 to 2021-08 | Professor (Department of Chemistry, Department of Chemical and Biological Engineering)
Employment
Source: Self-asserted source
Huang, Xuhui

The Hong Kong University of Science and Technology: Hong Kong, HK

2017-07 to 2019-06-30 | Padma Harilela Associate Professor of Science (Chemistry)
Employment
Source: Self-asserted source
Huang, Xuhui

Hong Kong University of Science and Technology: Kowloon, HK

2015-01-01 to 2019-06-30 | Associate Profrssor (Department of Chemistry, Department of Chemical and Biological Engineering)
Employment
Source: Self-asserted source
Huang, Xuhui

Hong Kong University of Science and Technology: Kowloon, HK

2010-01-10 to 2014-12-31 | Assistant Professor (Department of Chemistry)
Employment
Source: Self-asserted source
Huang, Xuhui

Stanford University: Stanford, CA, US

2008-09-01 to 2009-12-31 | Research Associate (Department of Bioengineering)
Employment
Source: Self-asserted source
Huang, Xuhui

Stanford University: Stanford, CA, US

2006-08-01 to 2008-09-01 | Simbios Distinguished Postdoctoral Fellow (Department of Bioengineering)
Employment
Source: Self-asserted source
Huang, Xuhui

Education and qualifications (2)

Columbia University: New York, NY, US

2001-09-01 to 2006-07-31 | PhD (Chemistry Department)
Education
Source: Self-asserted source
Huang, Xuhui

University of Science and Technology of China: Hefei, Anhui, CN

1997-09-01 to 2001-06-31 | B.S. (Department of Chemical Physics)
Education
Source: Self-asserted source
Huang, Xuhui

Works (50 of 178)

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Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

2024-11-16 | Preprint
Contributors: Yunrui Qiu; Shuming Liu; Xingcheng Lin; Ilona Christy Unarta; Xuhui Huang; Bin Zhang
Source: check_circle
Crossref

Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design

JACS Au
2024-10-28 | Journal article
Contributors: Yunrui Qiu; Rafal P. Wiewiora; Jesus A. Izaguirre; Huafeng Xu; Woody Sherman; Weiping Tang; Xuhui Huang
Source: check_circle
Crossref

Memory Kernel Minimization Based Neural Networks for Discovering Slow Collective Variables of Biomolecular Dynamics

2024-09-04 | Preprint
Contributors: Bojun Liu; Siqin Cao; Jordan G Boysen; Mingyi Xue; Xuhui Huang
Source: check_circle
Crossref

Human Replication Protein A complex is a Telomerase Processivity Factor Essential for Telomere Maintenance

2024-08-17 | Preprint
Contributors: Sourav Agrawal; Xiuhua Lin; Vivek Susvirkar; Michael S O'Connor; Bianca L Chavez; Victoria R Tholkes; Kaitlyn M Abe; Qixiang He; Xuhui Huang; Ci Ji Lim
Source: check_circle
Crossref

Replica Exchange with Solute Tempering for Protein Conformational Sampling

2024-08-09 | Preprint
Contributors: Yichong Lao; Michael O’Connor; Xuhui Huang
Source: check_circle
Crossref

FeatureDock: Protein-Ligand Docking Guided by Physicochemical Feature-Based Local Environment Learning using Transformer

2024-07-11 | Preprint
Contributors: Mingyi Xue; Bojun Liu; Siqin Cao; Xuhui Huang
Source: check_circle
Crossref

Information Bottleneck Approach for Markov Model Construction

Journal of Chemical Theory and Computation
2024-06-25 | Journal article
Contributors: Dedi Wang; Yunrui Qiu; Eric R. Beyerle; Xuhui Huang; Pratyush Tiwary
Source: check_circle
Crossref

Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design

2024-06-11 | Preprint
Contributors: Yunrui Qiu; Rafal P. Wiewiora; Jesus A. Izaguirre; Huafeng Xu; Woody Sherman; Weiping Tang; Xuhui Huang
Source: check_circle
Crossref

Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes

The Journal of Chemical Physics
2024-03-28 | Journal article
Contributors: Yue Wu; Siqin Cao; Yunrui Qiu; Xuhui Huang
Source: check_circle
Crossref

Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein–RNA Condensate

The Journal of Physical Chemistry B
2024-03-14 | Journal article
Contributors: Ilona C. Unarta; Siqin Cao; Eshani C. Goonetilleke; Jiani Niu; Samuel H. Gellman; Xuhui Huang
Source: check_circle
Crossref

Kinetic network models to elucidate aggregation dynamics of aggregation‐induced emission systems

Aggregate
2024-02 | Journal article
Contributors: Zige Liu; Michael L. Kalin; Bojun Liu; Siqin Cao; Xuhui Huang
Source: check_circle
Crossref

Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space

2024-01-23 | Preprint
Contributors: Bojun Liu; Jordan G. Boysen; Ilona Christy Unarta; Xuefeng Du; Yixuan Li; Xuhui Huang
Source: check_circle
Crossref

Ultrahigh-Throughput Directed Evolution of Polymer-Degrading Enzymes Using Yeast Display

Journal of the American Chemical Society
2023-12-20 | Journal article
Contributors: Mario A. Cribari; Maxwell J. Unger; Ilona C. Unarta; Ashley N. Ogorek; Xuhui Huang; Jeffrey D. Martell
Source: check_circle
Crossref

Sub-millisecond Atomistic Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate

2023-12-12 | Preprint
Contributors: Ilona C. Unarta; Siqin Cao; Eshani C. Goonetilleke; Jiani Niu; Samuel H. Gellman; Xuhui Huang
Source: check_circle
Crossref

Tutorials on How to Build Non-Markovian Dynamic Models from Molecular Dynamics Simulations for Studying Protein Dynamics

2023-11-28 | Preprint
Contributors: Yue Wu; Siqin Cao; Yunrui Qiu; Xuhui Huang
Source: check_circle
Crossref

Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels

The Journal of Chemical Physics
2023-10-07 | Journal article
Contributors: Siqin Cao; Yunrui Qiu; Michael L. Kalin; Xuhui Huang
Source: check_circle
Crossref

Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities

ACS Chemical Biology
2023-09-15 | Journal article
Contributors: Eric M. Kohn; Kirill Konovalov; Christian A. Gomez; Gillian N. Hoover; Andrew Kai-hei Yik; Xuhui Huang; Jeffrey D. Martell
Source: check_circle
Crossref

GraphVAMPnets for uncovering slow collective variables of self-assembly dynamics

The Journal of Chemical Physics
2023-09-07 | Journal article
Contributors: Bojun Liu; Mingyi Xue; Yunrui Qiu; Kirill A. Konovalov; Michael S. O’Connor; Xuhui Huang
Source: check_circle
Crossref

An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes

Journal of Chemical Theory and Computation
2023-07-25 | Journal article
Contributors: Yunrui Qiu; Michael S. O’Connor; Mingyi Xue; Bojun Liu; Xuhui Huang
Source: check_circle
Crossref

EPISOL: A software package with expanded functions to perform 3D‐RISM calculations for the solvation of chemical and biological molecules

Journal of Computational Chemistry
2023-06-30 | Journal article
Contributors: Siqin Cao; Michael L. Kalin; Xuhui Huang
Source: check_circle
Crossref

Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A

The Journal of Chemical Physics
2023-06-07 | Journal article
Contributors: Kirill A. Konovalov; Cheng-Guo Wu; Yunrui Qiu; Vijaya Kumar Balakrishnan; Pankaj Singh Parihar; Michael S. O’Connor; Yongna Xing; Xuhui Huang
Source: check_circle
Crossref

GraphVAMPnets for Uncovering Slow Collective Variables of Self-Assembly Dynamics

2023-05-18 | Preprint
Contributors: Bojun Liu; Mingyi Xue; Yunrui Qiu; Kirill Konovalov; Michael O’Connor; Xuhui Huang
Source: check_circle
Crossref

Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently

Journal of the American Chemical Society
2023-05-10 | Journal article
Contributors: Anthony J. Dominic, III; Siqin Cao; Andrés Montoya-Castillo; Xuhui Huang
Source: check_circle
Crossref

Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently

2023-04-27 | Preprint
Contributors: Anthony Dominic III; Siqin Cao; Andres Montoya-Castillo; Xuhui Huang
Source: check_circle
Crossref

Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations

Proceedings of the National Academy of Sciences
2023-03-21 | Journal article
Contributors: Anthony J. Dominic, III; Thomas Sayer; Siqin Cao; Thomas E. Markland; Xuhui Huang; Andrés Montoya-Castillo
Source: check_circle
Crossref

Nucleotide addition and cleavage by RNA polymerase II: Coordination of two catalytic reactions using a single active site

Journal of Biological Chemistry
2023-02 | Journal article
Contributors: Ilona Christy Unarta; Eshani C. Goonetilleke; Dong Wang; Xuhui Huang
Source: check_circle
Crossref

Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently

2023-01-30 | Preprint
Contributors: Anthony Dominic; Siqin Cao; Andres Montoya-Castillo; Xuhui Huang
Source: check_circle
Crossref

Integrative Generalized Master Equation: A Theory to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels

2023-01-17 | Preprint
Contributors: Siqin Cao; Yunrui Qiu; Michael Kalin; Xuhui Huang
Source: check_circle
Crossref

RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics

Physical Chemistry Chemical Physics
2022 | Journal article
Contributors: Hanlin Gu; Wei Wang; Siqin Cao; Ilona Christy Unarta; Yuan Yao; Fu Kit Sheong; Xuhui Huang
Source: check_circle
Crossref

Integrative Generalized Master Equation: A Theory to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels

2022-12-30 | Preprint
Contributors: Siqin Cao; Yunrui Qiu; Michael Kalin; Xuhui Huang
Source: check_circle
Crossref

The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules

The Journal of Physical Chemistry B
2022-11-03 | Journal article
Contributors: Siqin Cao; Yunrui Qiu; Ilona C. Unarta; Eshani C. Goonetilleke; Xuhui Huang
Source: check_circle
Crossref

EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules

2022-10-31 | Preprint
Contributors: Siqin Cao; Michael Kalin; Xuhui Huang
Source: check_circle
Crossref

Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations

2022-10-20 | Preprint
Contributors: Anthony J. Dominic, III; Thomas Sayer; Siqin Cao; Thomas E. Markland; Xuhui Huang; Andrés Montoya-Castillo
Source: check_circle
Crossref

Kinetic network models to study molecular self-assembly in the wake of machine learning

MRS Bulletin
2022-09 | Journal article
Contributors: Bojun Liu; Yunrui Qiu; Eshani C. Goonetilleke; Xuhui Huang
Source: check_circle
Crossref

A Step-by-step Guide on How to Construct quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules

2022-02-17 | Preprint
Contributors: Andrew Kai-hei Yik; Yunrui Qiu; Ilona Christy Unarta; Siqin Cao; Xuhui Huang
Source: check_circle
Crossref

1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication

Physical Chemistry Chemical Physics
2021 | Journal article
Contributors: Lu Zhang; Dong Zhang; Xiaowei Wang; Congmin Yuan; Yongfang Li; Xilin Jia; Xin Gao; Hui-Ling Yen; Peter Pak-Hang Cheung; Xuhui Huang
Source: check_circle
Crossref

Construction of diverse peptide structural architectures via chemoselective peptide ligation

Chemical Science
2021 | Journal article
Contributors: Carina Hey Pui Cheung; Jianchao Xu; Chi Lung Lee; Yanfeng Zhang; Ruohan Wei; Donald Bierer; Xuhui Huang; Xuechen Li
Source: check_circle
Crossref

Incorporation efficiency and inhibition mechanism of 2′-substituted nucleotide analogs against SARS-CoV-2 RNA-dependent RNA polymerase

Physical Chemistry Chemical Physics
2021 | Journal article
Part of ISSN: 1463-9076
Part of ISSN: 1463-9084
Source: Self-asserted source
Huang, Xuhui
grade
Preferred source (of 2)‎

Microsecond timescale MD simulations at the transition state of PmHMGR predict remote allosteric residues

Chemical Science
2021 | Journal article
Contributors: Taylor R. Quinn; Calvin N. Steussy; Brandon E. Haines; Jinping Lei; Wei Wang; Fu Kit Sheong; Cynthia V. Stauffacher; Xuhui Huang; Per-Ola Norrby; Paul Helquist et al.
Source: check_circle
Crossref

Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex

Communications Biology
2021-11-30 | Journal article
Contributors: Lizhe Zhu; Hanlun Jiang; Siqin Cao; Ilona Christy Unarta; Xin Gao; Xuhui Huang
Source: check_circle
Crossref

Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning

JACS Au
2021-09-27 | Journal article
Contributors: Kirill A. Konovalov; Ilona Christy Unarta; Siqin Cao; Eshani C. Goonetilleke; Xuhui Huang
Source: check_circle
Crossref

A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase

Nucleic Acids Research
2021-09-07 | Journal article
Contributors: 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
Source: check_circle
Crossref

Role of Surface Templating on Ice Nucleation Efficiency on a Silver Iodide Surface

The Journal of Physical Chemistry C
2021-09-02 | Journal article
Contributors: Zhuo Liu; Chu Li; Eshani C. Goonetilleke; Yi Cui; Xuhui Huang
Source: check_circle
Crossref

Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation

Nature Communications
2021-08-16 | Journal article
Contributors: Chu Li; Zhuo Liu; Eshani C. Goonetilleke; Xuhui Huang
Source: check_circle
Crossref

ChemPLAN-Net: A deep learning framework to find novel inhibitor fragments for proteins

2021-08-08 | Other
Contributors: Michael A. Suarez Vasquez; Mingyi Xue; Jordy H. Lam; Eshani C. Goonetilleke; Xin Gao; Xuhui Huang
Source: check_circle
Crossref

RPnet: A Reverse Projection Based Neural Network for Coarse-graining Metastable Conformational States for Protein Dynamics

2021-08-06 | Other
Contributors: Hanlin Gu; Wei Wang; Siqin Cao; Ilona Christy Unarta; Yuan Yao; Fu Kit Sheong; Xuhui Huang
Source: check_circle
Crossref

Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Simulation Trajectories

2021-06-10 | Other
Contributors: Song Liu; Siqin Cao; Michael Suarez; Eshani C. Goonetillek; Xuhui Huang
Source: check_circle
Crossref

An Efficient Method to Quantify Structural Distributions in Heterogeneous cryo-EM Datasets

2021-05-28 | Other
Contributors: Hanlin Gu; Wei Wang; Ilona Christy Unarta; Wenqi Zeng; Fu Kit Sheong; Peter Pak-Hang Cheung; Song Liu; Yuan Yao; Xuhui Huang
Source: check_circle
Crossref

Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models

Current Opinion in Structural Biology
2021-04 | Journal article
Contributors: Xiaowei Wang; Ilona Christy Unarta; Peter Pak-Hang Cheung; Xuhui Huang
Source: check_circle
Crossref

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
2021-04-27 | Journal article
Contributors: Ilona Christy Unarta; Siqin Cao; Shintaroh Kubo; Wei Wang; Peter Pak-Hang Cheung; Xin Gao; Shoji Takada; Xuhui Huang
Source: check_circle
Crossref
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Peer review (81 reviews for 19 publications/grants)

Review activity for ACS catalysis. (6)
Review activity for ACS central science. (3)
Review activity for Analytical chemistry. (1)
Review activity for Biochemistry. (1)
Review activity for Chemical research in toxicology. (2)
Review activity for Communications chemistry. (1)
Review activity for eLife (1)
Review activity for Journal of chemical information and modeling. (12)
Review activity for Journal of chemical physics. (5)
Review activity for Journal of chemical theory and computation : (17)
Review activity for Journal of physical chemistry. (1)
Review activity for Journal of the American Chemical Society. (4)
Review activity for Macromolecules. (1)
Review activity for Nature chemistry. (1)
Review activity for Nature communications (9)
Review activity for Nature computational science. (1)
Review activity for PLoS computational biology. (3)
Review activity for The journal of physical chemistry. (10)
Review activity for The journal of physical chemistry. (2)