Author details

Full Name

Xuhui Huang

Affiliation

ORCID

Career Start Year

2004

Papers

129

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36581202	Nucleotide addition and cleavage by RNA polymerase II: Coordination of two catalytic reactions using a single active site.		2023
34985469	RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics.	Physical Chemistry Chemical Physics	2022
35298336	Elucidation of the key role of PtÂ·Â·Â·Pt interactions in the directional self-assembly of platinum(II) complexes.	Proceedings of the National Academy of Sciences of the United States of America	2022
34379778	A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase.	Nucleic Acids Research	2021
34237555	The mechanism of action of T-705 as a unique delayed chain terminator on influenza viral polymerase transcription.	Biophysical Chemistry	2021
34123337	Construction of diverse peptide structural architectures chemoselective peptide ligation.	Chemical Science	2021
33688867	1'-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication.	Phys Chem Chem Phys	2021
33732808	EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error.	Bio-protocol	2021
33883282	Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.	Proc Natl Acad Sci U S A	2021
33991521	A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models.	Journal of Biological Chemistry	2021
34140682	Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.	Nat Chem Biol	2021
34084441	Microsecond timescale MD simulations at the transition state of HMGR predict remote allosteric residues.	Chemical Science	2021
33126140	Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models.	Current Opinion in Structural Biology	2021
33169432	Are endoplasmic reticulum subdomains shaped by asymmetric distribution of phospholipids? Evidence from a C. elegans model system.	BioEssays	2021
34514487	Incorporation efficiency and inhibition mechanism of 2'-substituted nucleotide analogs against SARS-CoV-2 RNA-dependent RNA polymerase.	Physical Chemistry Chemical Physics	2021
34458841	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	2021
34400646	Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation.	Nature Communications	2021
34848812	Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex.	Commun Biol	2021
34604842	Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning.		2021
32576842	The hydrolytic water molecule of Class A Î²-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis.	Scientific Reports	2020
32325070	Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling.	Journal of Molecular Biology	2020
32251767	Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro.	Antiviral Research	2020
31985176	Corrigendum: Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis.	Angew Chem Int Ed Engl	2020
32389636	Molecular basis defining the selectivity of substituted isoquinolinones for the melatonin MT receptor.	Biochemical Pharmacology	2020
31976572	Three-site and five-site fixed-charge water models compatible with AMOEBA force field.	Journal of Computational Chemistry	2020
32820079	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	2020
32640825	On the advantages of exploiting memory in Markov state models for biomolecular dynamics.	Journal of Chemical Physics	2020
31340641	Specific and Quantitative Detection of Albumin in Biological Fluids by Tetrazolate-Functionalized Water-Soluble AIEgens.	ACS applied materials & interfaces	2019
31666519	A deep learning framework to predict binding preference of RNA constituents on protein surface.	Nat Commun	2019
30591565	Two symmetric arginine residues play distinct roles in <i>Thermus thermophilus</i> Argonaute DNA guide strand-mediated DNA target cleavage.	Proc Natl Acad Sci U S A	2019
30927873	TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules.	Journal of Chemical Physics	2019
31179024	Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate.	Nat Energy	2019
31273202	Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process.	Nature Communications	2019
31016302	A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: regulation and robustness of energy transfer pathways.	Faraday Discussions	2019
31065519	Mechanistic Insights and Rational Design of a Versatile Surface with Cells/Bacteria Recognition Capability via Orientated Fusion Peptides.	Advanced Science	2019
30718278	8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II.	Journal of Biological Chemistry	2019
29414512	Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models.	Current Opinion in Structural Biology	2018
30578407	Conformational selection turns on phenylalanine hydroxylase.	Journal of Biological Chemistry	2018
30134698	An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling.	Journal of Chemical Physics	2018
30412395	DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery.	Journal of the American Chemical Society	2018
29620122	Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways.	Physical Chemistry Chemical Physics	2018
29479585	Harnessing complexity in molecular self-assembly using computer simulations.	Physical Chemistry Chemical Physics	2018
29478808	Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.	Molecular Cell	2018
29743517	Identification of new EphA4 inhibitors by virtual screening of FDA-approved drugs.	Scientific Reports	2018
29158257	Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk.	Journal of Biological Chemistry	2018
28100776	Crystallographic Snapshots of Class A Î²-Lactamase Catalysis Reveal Structural Changes That Facilitate Î²-Lactam Hydrolysis.	Journal of Biological Chemistry	2017
28732205	Unique Roles of the Non-identical MCM Subunits in DNA Replication Licensing.	Molecular Cell	2017
28692263	Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers.	Journal of the American Chemical Society	2017
28507673	AIEgen-based theranostic system: targeted imaging of cancer cells and adjuvant amplification of antitumor efficacy of paclitaxel.	Chemical Science	2017
28953867	Massively parallel de novo protein design for targeted therapeutics.	Nature	2017