2024 article
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization
Lin, X., & Zhang, B. (2024, January 10).
2024 journal article
Explicit ion modeling predicts physicochemical interactions for chromatin organization
ELife.
2024 article
Interpretable Protein-DNA Interactions Captured by Structure-based Optimization
Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2024, May 27).
2024 journal article
RACER-m leverages structural features for sparse T cell specificity prediction
SCIENCE ADVANCES, 10(20).
2024 journal article
Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies
BIOPHYSICAL JOURNAL, 123(6), 681–692.
2023 article
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization
Lin, X., & Zhang, B. (2023, May 18).
2023 article
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization
Lin, X., & Zhang, B. (2023, August 21).
2023 journal article
Explicit ion modeling predicts physicochemical interactions for chromatin organization
ELIFE, 12.
2023 article
RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction
Wang, A., Lin, X., Chau, K. N., Onuchic, J. N., Levine, H., & George, J. T. (2023, August 7). (Vol. 8). Vol. 8.
2023 article
Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity
Guo, J., Chen, X., Manna, P., Lin, X., Scott, M. N., Chen, W. J., … Schlau-Cohen, G. S. (2023, March 16).
2022 journal article
Chromatin fiber breaks into clutches under tension and crowding
Nucleic Acids Research, 50(17), 9738–9747.
2022 journal article
Contact map dependence of a T-cell receptor binding repertoire
Physical Review E.
2022 journal article
Ligand-induced transmembrane conformational coupling in monomeric EGFR
Nature Communications, 13(1).
2021 article
Chromatin fiber breaks into clutches under tension and crowding
Liu, S., Lin, X., & Zhang, B. (2021, November 18). (Vol. 11). Vol. 11.
2021 journal article
Cooperative DNA looping by PRC2 complexes
Nucleic Acids Research, 49(11), 6238–6248.
2021 journal article
Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms
Journal of Chemical Theory and Computation, 17(5), 3178–3187.
2021 article
Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms
Antonio B. Oliveira, J., Lin, X., Kulkarni, P., Onuchic, J. N., Roy, S., & Leite, V. B. P. (2021, January 29).
2021 article
Ligand-induced transmembrane conformational coupling in monomeric EGFR
Srinivasan, S., Regmi, R., Lin, X., Dreyer, C. A., Chen, X., Quinn, S. D., … Schlau-Cohen, G. S. (2021, October 28). (Vol. 10). Vol. 10.
2021 journal article
Multiscale modeling of genome organization with maximum entropy optimization
The Journal of Chemical Physics, 155(1), 010901.
2021 journal article
Rapid assessment of T-cell receptor specificity of the immune repertoire
Nature Computational Science, 1(5), 362–373.
2021 journal article
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Nature Communications, 12(1).
2021 article
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Ding, X., Lin, X., & Zhang, B. (2021, January 8).
2020 journal article
Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry
Nature Communications, 11(1).
2020 journal article
Molecular-replacement phasing using predicted protein structures from <i>AWSEM-Suite
IUCrJ, 7(6), 1168–1178.
2020 journal article
Protein Structure Prediction in CASP13 Using AWSEM-Suite
Journal of Chemical Theory and Computation, 16(6), 3977–3988.
2020 journal article
Protein Structure Refinement Guided by Atomic Packing Frustration Analysis
The Journal of Physical Chemistry B, 124(48), 10889–10898.
2020 journal article
Rapid assessment of T-cell receptor specificity of the immune repertoire
Nature Computational Science.
2020 journal article
Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin
Proceedings of the National Academy of Sciences, 117(48), 30465–30475.
2019 journal article
Forging tools for refining predicted protein structures
Proceedings of the National Academy of Sciences, 116(19), 9400–9409.
2019 journal article
Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins
Biomolecules, 9(4), 146.
2019 journal article
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level
Biomolecules, 9(2), 77.
2018 journal article
Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill
Proceedings of the National Academy of Sciences, 115(34).
2018 journal article
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer
Journal of Molecular Biology, 430(16), 2422–2438.
Contributors: , S. Roy *, M. Jolly *, F. Bocci *, N. Schafer *, M. Tsai *, Y. Chen *, Y. He * *
2018 article
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer
Lin, X., Roy, S., Jolly, M. K., Bocci, F., Schafer, N., Tsai, M.-Y., … Onuchic, J. N. (2018, February 14). (Vol. 2). Vol. 2.
2018 journal article
Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields
Journal of Chemical Theory and Computation, 14(11), 6102–6116.
2017 journal article
Quantum Image Processing and Its Application to Edge Detection: Theory and Experiment
Physical Review X, 7(3).
2016 journal article
Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin
The Journal of Physical Chemistry B, 120(36), 9654–9660.
Contributors: , J. Noel *, Q. Wang *, J. Ma * & J. Onuchic * *
2016 journal article
Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins
The Journal of Physical Chemistry B, 121(15), 3473–3482.
Contributors: M. Chen *, * , W. Lu *, J. Onuchic * & P. Wolynes *
2016 journal article
Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model
The Journal of Physical Chemistry B, 120(33), 8557–8565.
Contributors: M. Chen *, * , W. Zheng *, J. Onuchic * & P. Wolynes *
2014 journal article
Order and disorder control the functional rearrangement of influenza hemagglutinin
Proceedings of the National Academy of Sciences, 111(33), 12049–12054.
Contributors: , N. Eddy*, J. Noel *, P. Whitford *, Q. Wang *, J. Ma *, J. Onuchic * *
2010 journal article
Measurement method of logical gate in bulk spin quantum computer
Wuhan Ligong Daxue Xuebao/Journal of Wuhan University of Technology, 32(15), 142–145.
2010 journal article
Subspace quantum process tomography via nuclear magnetic resonance
Acta Physica Sinica, 59(10), 6837.
Updated: July 20th, 2023 10:51
2023 - present
2018 - 2023
2018 - 2018
Updated: February 11th, 2018 23:45
2011 - present
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