Qiang Cui

Biochemistry, Genetics and Molecular BiologyPhysics and Astronomy

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 64 papers. Top paper: “Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations”.

Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.06.017

N/A

0.968DataRank · unranked

34 citations

Taraknath Mandal, Matthew R. Elkins, Younghoon Oh, Qiang Cui, Mei Hong +1 more

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

Nature Communications(2021)10.1038/s41467-021-22665-4

N/A

0.722DataRank · unranked

122 citations

Huitao Fan, Sara A. Grimm, Jae Jin Kim, Linhui Li, Yiran Guo +21 more

Artificial Intracellular Filaments

Cell Reports Physical Science(2020)10.1016/j.xcrp.2020.100085

N/A

0.646DataRank · unranked

73 citations

Huaimin Wang, Fengbin Wang, Younghoon Oh, Cristina Berciu, Qiang Cui +3 more

Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines

Annual Review of Biophysics(2023)10.1146/annurev-biophys-111622-091140

N/A

0.574DataRank · unranked

45 citations

Marcus Elstner, Qiang Cui, Tomáš Kubař

Anionic nanoparticle-induced perturbation to phospholipid membranes affects ion channel function

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2004736117

N/A

0.568DataRank · unranked

43 citations

Dongyue Liang, Elizabeth D. Laudadio, Jorge D. Calderin, Meng Wu, Puspam Keshri +8 more

Implications for an Imidazole-2-yl Carbene Intermediate in the Rhodanase-Catalyzed C–S Bond Formation Reaction of Anaerobic Ergothioneine Biosynthesis

ACS Catalysis(2021)10.1021/acscatal.0c04886

N/A

0.470DataRank · unranked

22 citations

Rui Lai, Chao Peng, Juan Lopez, Zhihong Li, Nathchar Naowarojna +10 more

Influence of Surface Ligand Molecular Structure on Phospholipid Membrane Disruption by Cationic Nanoparticles

Langmuir(2021)10.1021/acs.langmuir.1c01146

N/A

0.425DataRank · unranked

16 citations

Udaya Dahal, Z. Vivian Feng, Zeev Rosenzweig, Qiang Cui, Robert J. Hamers +1 more

Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA

Journal of the American Chemical Society(2023)10.1021/jacs.3c02423

N/A

0.416DataRank · unranked

15 citations

Qiang Cui, Jiahua Deng

Thermodynamic analysis of the GASright transmembrane motif supports energetic model of dimerization

Biophysical Journal(2022)10.1016/j.bpj.2022.11.018

N/A

0.405DataRank · unranked

10 citations

Qiang Cui, Alessandro Senes, Gladys Díaz Vázquez

Cholesterol-Mediated Clustering of the HIV Fusion Protein gp41 in Lipid Bilayers

Journal of Molecular Biology(2021)10.1016/j.jmb.2021.167345

N/A

0.396DataRank · unranked

13 citations

Younghoon Oh, Madeleine Sutherland, Qiang Cui, Mei Hong, Nhi Tran

Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00591

N/A

0.373DataRank · unranked

11 citations

Qiang Cui, Yuchen Yuan

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(2023)10.1073/pnas.2310727120

N/A

0.360DataRank · unranked

10 citations

Vijaya Kumar Balakrishnan, Ronald A. Merrill, Pankaj Singh Parihar, Kirill Konovolov, Yu‐Chia Chen +14 more

Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.168998

N/A

0.269DataRank · unranked

5 citations

Qiang Cui

A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery

eLife(2023)10.7554/elife.92262

N/A

0.241DataRank · unranked

4 citations

Thomas Gillis, Srivatsan Raman, Qiang Cui, Zhuang Liu

Toward Improving Multiple Time Step QM/MM Simulations with Δ-Machine Learning

The Journal of Physical Chemistry B(2025)10.1021/acs.jpcb.5c05255

N/A

0.241DataRank · unranked

4 citations

Kwangho Nam, Qiang Cui, Reilly Osadchey

The catalytic mechanism of the RNA methyltransferase METTL3

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.06.556513

N/A

0.104DataRank · unranked

1 citations

Pablo Andrés Vargas-Rosales, R.K. Bedi, Jiahua Deng, Dylan Coelho, Emmanuelle Braud +7 more

Molecular mechanism of GTP binding- and dimerization-induced enhancement of Sar1-mediated membrane remodeling

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.20.500836

N/A

0.104DataRank · unranked

1 citations

Anjon Audhya, Qiang Cui, Sanjoy Paul

Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions

Biophysics Reviews(2025)10.1063/5.0248589

N/A

0.104DataRank · unranked

1 citations

Qiang Cui

A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.06.552196

N/A

0.104DataRank · unranked

1 citations

Thomas Gillis, Srivatsan Raman, Qiang Cui, Zhuang Liu

The catalytic mechanism of the RNA methyltransferase METTL3

eLife(2023)10.7554/elife.92537

N/A

0DataRank · unranked

35 citations

Pablo Andrés Vargas-Rosales, R.K. Bedi, Jiahua Deng, Dylan Coelho, Emmanuelle Braud +7 more

Molecular mechanism of GTP binding- and dimerization-induced enhancement of Sar1-mediated membrane remodeling

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2212513120

N/A

0DataRank · unranked

23 citations

Anjon Audhya, Qiang Cui, Sanjoy Paul

Multipole Expansion of Atomic Electron Density Fluctuation Interactions in the Density-Functional Tight-Binding Method

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00778

N/A

0DataRank · unranked

10 citations

Bálint Aradi, Anders M. N. Niklasson, Qiang Cui, Stephan Irle, Van‐Quan Vuong

Synaptotagmin-7 outperforms synaptotagmin-1 to promote the formation of large, stable fusion pores via robust membrane penetration

Nature Communications(2023)10.1038/s41467-023-42497-8

N/A

0DataRank · unranked

6 citations

Taraknath Mandal, Nikunj Mehta, Lanxi Wu, Yueqi Li, Debasis Das +3 more

Reparameterization of the chemical-potential equalization model with DFTB3: A practical balance between accuracy and transferability

The Journal of Chemical Physics(2023)10.1063/5.0132903

N/A

0DataRank · unranked

4 citations

Qiang Cui, Van‐Quan Vuong

The catalytic mechanism of the RNA methyltransferase METTL3

HAL (Le Centre pour la Communication Scientifique Directe)(2023)10.7554/elife.92537.1

N/A

0DataRank · unranked

2 citations

Pablo Andrés Vargas-Rosales, R.K. Bedi, Jiahua Deng, Dylan Coelho, Emmanuelle Braud +7 more

A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery

(2023)10.7554/elife.92262.1

N/A

0DataRank · unranked

1 citations

Thomas Gillis, Srivatsan Raman, Qiang Cui, Zhuang Liu

Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56δ holoenzyme

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.09.530109

N/A

0DataRank · unranked

0 citations

Vijaya Kumar Balakrishnan, Pankaj Singh Parihar, Kirill Konovolov, Yu‐Chia Chen, Ronald A. Merrill +14 more

The juxtamembrane linker of synaptotagmin 1 regulates Ca 2+ binding via liquid-liquid phase separation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.11.551903

N/A

0DataRank · unranked

0 citations

Sayantan Mondal, Emma T. Watson, Qiang Cui, Edwin R. Chapman, Nikunj Mehta

Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.29.555381

N/A

0DataRank · unranked

0 citations

Yuchen Yuan, Qiang Cui, Jiahua Deng

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04100

N/A

0DataRank · unranked

116 citations

Steven L. Austin, Arnaud Blondel, Eric D. Boittier, Stefan Boresch, Matthias Buck +68 more

The juxtamembrane linker of synaptotagmin 1 regulates Ca2+ binding via liquid-liquid phase separation

Nature Communications(2024)10.1038/s41467-023-44414-5

N/A

0DataRank · unranked

28 citations

Sayantan Mondal, Emma T. Watson, Qiang Cui, Edwin R. Chapman, Nikunj Mehta

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins

Journal of the American Chemical Society(2024)10.1021/jacs.3c13981

N/A

0DataRank · unranked

17 citations

Guohui Li, Qiang Cui, Rui Lai

Electronic Polarization Leads to a Drier Dewetted State for Hydrophobic Gating in the Big Potassium Channel

The Journal of Physical Chemistry Letters(2024)10.1021/acs.jpclett.4c01359

N/A

0DataRank · unranked

13 citations

Qiang Cui, Jiahua Deng

Complete Computational Reaction Mechanism for Foldamer-Catalyzed Aldol Condensation

ACS Catalysis(2024)10.1021/acscatal.4c00937

N/A

0DataRank · unranked

10 citations

Darren Demapan, Qiang Cui, Reilly Osadchey Brown

Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR

Journal of the American Chemical Society(2024)10.1021/jacs.3c12494

N/A

0DataRank · unranked

9 citations

Yuchen Yuan, Qiang Cui, Jiahua Deng

The catalytic mechanism of the RNA methyltransferase METTL3

eLife(2024)10.7554/elife.92537.3

N/A

0DataRank · unranked

3 citations

Pablo Andrés Vargas-Rosales, R.K. Bedi, Jiahua Deng, Dylan Coelho, Emmanuelle Braud +7 more

Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00013

N/A

0DataRank · unranked

6 citations

Qiang Cui, Jiahua Deng

A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery

eLife(2024)10.7554/elife.92262.3

N/A

0DataRank · unranked

5 citations

Thomas Gillis, Srivatsan Raman, Qiang Cui, Zhuang Liu

Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.08.584185

N/A

0DataRank · unranked

3 citations

Harini A. Perera, Rylie Bolarinho, Zeke A. Piskulich, Zhongyue Guo, Jiaze Yin +8 more

eLife Assessment: Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists

(2024)10.7554/elife.95992.1.sa3

N/A

0DataRank · unranked

0 citations

Qiang Cui

eLife Assessment: N-acetylation of α-synuclein enhances synaptic vesicle clustering mediated by α-synuclein and lysophosphatidylcholine

(2024)10.7554/elife.97228.1.sa2

N/A

0DataRank · unranked

0 citations

Qiang Cui

Recent Developments in DFTB+, a Software Package for Efficient Atomistic Quantum Mechanical Simulations

The Journal of Physical Chemistry A(2025)10.1021/acs.jpca.5c01146

N/A

0DataRank · unranked

19 citations

Matías Berdakin, J. A. Bich, Franco P. Bonafé, Cristopher Camacho, Qiang Cui +27 more

Approaches for regulating enzyme activities: Recent advances in experiment and computation

Current Opinion in Structural Biology(2025)10.1016/j.sbi.2025.103124

N/A

0DataRank · unranked

3 citations

Qiang Cui

Impact of Fluctuations in the Peridinin-Chlorophyll a-Protein on the Energy Transfer: Insights from Classical and QM/MM Molecular Dynamics Simulations

Biochemistry(2025)10.1021/acs.biochem.4c00568

N/A

0DataRank · unranked

3 citations

Qiang Cui, M.V. Sokolov

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence

Chemical Science(2020)10.1039/d0sc05743f

N/A

0DataRank · unranked

127 citations

Xiaoxiao Yao, Meng Wu, Arielle C. Mensch, Yi Cui, Jiahua Deng +15 more

New and notable: Polarizing phosphorylated proteins

Biophysical Journal(2025)10.1016/j.bpj.2025.11.022

N/A

0DataRank · unranked

0 citations

Qiang Cui, Sangram Prusty

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2009316117

N/A

0DataRank · unranked

116 citations

Huitao Fan, Sara A. Grimm, Yiran Guo, Jae Jin Kim, Jiekai Yin +20 more

Photo‐Disassembly of Membrane Microdomains Revives Conventional Antibiotics against MRSA

Advanced Science(2020)10.1002/advs.201903117

N/A

0DataRank · unranked

61 citations

Pu‐Ting Dong, Lijia Liang, Taraknath Mandal, Junjie Li, Erlinda R. Ulloa +8 more

Multi-level free energy simulation with a staged transformation approach

The Journal of Chemical Physics(2020)10.1063/5.0012494

N/A

0DataRank · unranked

20 citations

Qiang Cui, Shingo Ito

Improvement of d–d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+ U model on nickel coordination compounds

Physical Chemistry Chemical Physics(2020)10.1039/d0cp04694a

N/A

0DataRank · unranked

6 citations

Rui Lai, Marcus Elstner, Maja Gruden, Pablo García‐Fernández, Qiang Cui +1 more

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.27.064493

N/A

0DataRank · unranked

11 citations

Huitao Fan, Sara A. Grimm, Yiran Guo, Jae Jin Kim, Linhui Li +20 more

Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.10.942417

N/A

0DataRank · unranked

2 citations

Yuchen Yuan, Anthony Meger, Qiang Cui, Srivatsan Raman, Megan Leander

Substrate deformation regulates DRM2-mediated DNA methylation in plants

(2020)10.1101/2020.03.17.995522

N/A

0DataRank · unranked

1 citations

Sarah M. Leichter, Jianjun Jiang, Mahamaya Biswal, Jiuwei Lu, Zhimin Zhang +6 more

Substrate deformation regulates DRM2-mediated DNA methylation in plants

Science Advances(2021)10.1126/sciadv.abd9224

N/A

0DataRank · unranked

32 citations

Sarah M. Leichter, Jianjun Jiang, Mahamaya Biswal, Jiuwei Lu, Zhimin Zhang +6 more

O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2024803118

N/A

0DataRank · unranked

17 citations

Thilo Mast, Marcus Elstner, Qiang Cui, Tomáš Kubař, Denis Maag

The coiled-coil domain of Escherichia coli FtsLB is a structurally detuned element critical for modulating its activation in bacterial cell division

Journal of Biological Chemistry(2021)10.1016/j.jbc.2021.101460

N/A

0DataRank · unranked

13 citations

Samson G.F. Condon, Gladys Díaz Vázquez, Qiang Cui, Alessandro Senes, Samuel Craven

The coiled-coil domain of E. coli FtsLB is a structurally detuned element critical for modulating its activation in bacterial cell division

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.21.440662

N/A

0DataRank · unranked

0 citations

Samson G.F. Condon, Gladys Díaz Vázquez, Qiang Cui, Alessandro Senes, Samuel Craven

Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins

eLife(2022)10.7554/elife.79932

N/A

0DataRank · unranked

53 citations

Zhuang Liu, Qiang Cui, Srivatsan Raman, Megan Leander

The complexin C-terminal amphipathic helix stabilizes the fusion pore open state by sculpting membranes

Nature Structural & Molecular Biology(2022)10.1038/s41594-021-00716-0

N/A

0DataRank · unranked

42 citations

Lanxi Wu, Taraknath Mandal, Mark F. Swift, Zhao Zhang, Mohammad Alaghemandi +10 more

Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process

Journal of Computational Chemistry(2022)10.1002/jcc.26846

N/A

0DataRank · unranked

18 citations

Juan Zeng, Fei Xia, Qiang Cui, Xianming Deng, Xin Xu +1 more

Identification of functional substates of KRas during GTP hydrolysis with enhanced sampling simulations

Physical Chemistry Chemical Physics(2022)10.1039/d2cp00274d

N/A

0DataRank · unranked

18 citations

Jian Chen, Fei Xia, Qiang Cui, Xianming Deng, Xin Xu +1 more

Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.01.490188

N/A

0DataRank · unranked

0 citations

Zhuang Liu, Qiang Cui, Srivatsan Raman, Megan Leander

Synaptotagmin 7 outperforms synaptotagmin 1 to promote the formation of large, stable fusion pores via robust membrane penetration

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.07.499215

N/A

0DataRank · unranked

0 citations

Taraknath Mandal, Nikunj Mehta, Lanxi Wu, Yueqi Li, Debasis Das +3 more

Thermodynamic analysis of the GAS right transmembrane motif supports energetic model of dimerization

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.11.499632

N/A

0DataRank · unranked

0 citations

Qiang Cui, Alessandro Senes, Gladys Díaz Vázquez