Xingcheng Lin

Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions

Li, R., & Lin, X. (2024, October 13).

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

Lin, X., & Zhang, B. (2024, January 10).

Explicit ion modeling predicts physicochemical interactions for chromatin organization

ELife.

Interpretable Protein-DNA Interactions Captured by Structure-based Optimization

Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2024, May 27).

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

Qiu, Y., Liu, S., Lin, X., Unarta, I. C., Huang, X., & Zhang, B. (2024, November 16).

RACER-m leverages structural features for sparse T cell specificity prediction

SCIENCE ADVANCES, 10(20).

Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies

BIOPHYSICAL JOURNAL, 123(6), 681–692.

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

Lin, X., & Zhang, B. (2023, May 18).

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

Lin, X., & Zhang, B. (2023, August 21).

Explicit ion modeling predicts physicochemical interactions for chromatin organization

ELIFE, 12.

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.

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).

Chromatin fiber breaks into clutches under tension and crowding

Nucleic Acids Research, 50(17), 9738–9747.

Contact map dependence of a T-cell receptor binding repertoire

Physical Review E.

Ligand-induced transmembrane conformational coupling in monomeric EGFR

Nature Communications, 13(1).

Chromatin fiber breaks into clutches under tension and crowding

Liu, S., Lin, X., & Zhang, B. (2021, November 18). (Vol. 11). Vol. 11.

Cooperative DNA looping by PRC2 complexes

Nucleic Acids Research, 49(11), 6238–6248.

Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms

Journal of Chemical Theory and Computation, 17(5), 3178–3187.

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).

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.

Multiscale modeling of genome organization with maximum entropy optimization

The Journal of Chemical Physics, 155(1), 010901.

Rapid assessment of T-cell receptor specificity of the immune repertoire

Nature Computational Science, 1(5), 362–373.

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

Nature Communications, 12(1).

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

Ding, X., Lin, X., & Zhang, B. (2021, January 8).

Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry

Nature Communications, 11(1).

Molecular-replacement phasing using predicted protein structures from <i>AWSEM-Suite

IUCrJ, 7(6), 1168–1178.

Protein Structure Prediction in CASP13 Using AWSEM-Suite

Journal of Chemical Theory and Computation, 16(6), 3977–3988.

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

The Journal of Physical Chemistry B, 124(48), 10889–10898.

Rapid assessment of T-cell receptor specificity of the immune repertoire

Nature Computational Science.

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.

Forging tools for refining predicted protein structures

Proceedings of the National Academy of Sciences, 116(19), 9400–9409.

Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins

Biomolecules, 9(4), 146.

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Biomolecules, 9(2), 77.

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).

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

Journal of Molecular Biology, 430(16), 2422–2438.

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.

Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields

Journal of Chemical Theory and Computation, 14(11), 6102–6116.

Quantum Image Processing and Its Application to Edge Detection: Theory and Experiment

Physical Review X, 7(3).

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.

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.

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.

Order and disorder control the functional rearrangement of influenza hemagglutinin

Proceedings of the National Academy of Sciences, 111(33), 12049–12054.

Measurement method of logical gate in bulk spin quantum computer

Wuhan Ligong Daxue Xuebao/Journal of Wuhan University of Technology, 32(15), 142–145.

Subspace quantum process tomography via nuclear magnetic resonance

Acta Physica Sinica, 59(10), 6837.