Xingcheng Lin

Lin, X., & Zhang, B. (2024, January 10). Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. https://doi.org/10.7554/eLife.90073.2

Lin, X., & Zhang, B. (2024). Explicit ion modeling predicts physicochemical interactions for chromatin organization. ELife. https://doi.org/10.7554/eLife.90073.3

Lin, X., & Zhang, B. (2024). Explicit ion modeling predicts physicochemical interactions for chromatin organization. ELIFE, 12. https://doi.org/10.7554/eLife.90073

Lin, X., & Zhang, B. (2023, May 18). Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. https://doi.org/10.1101/2023.05.16.541030

Lin, X., & Zhang, B. (2023, August 21). Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. https://doi.org/10.7554/eLife.90073.1

Wang, A., Lin, X., Chau, K. N., Onuchic, J. N., Levine, H., & George, J. T. (2023, August 7). RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction (Vol. 8). Vol. 8. https://doi.org/10.1101/2023.08.06.552190

Guo, J., Chen, X., Manna, P., Lin, X., Scott, M. N., Chen, W. J., … Schlau-Cohen, G. S. (2023, March 16). Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity. https://doi.org/10.1101/2023.03.15.532809

Liu, S., Lin, X., & Zhang, B. (2022). Chromatin fiber breaks into clutches under tension and crowding. Nucleic Acids Research, 50(17), 9738–9747. https://doi.org/10.1093/nar/gkac725

Chau, K. N., George, J. T., Onuchic, J. N., Lin, X., & Levine, H. (2022). Contact map dependence of a T-cell receptor binding repertoire. Physical Review E. https://doi.org/10.1103/PhysRevE.106.014406

Srinivasan, S., Regmi, R., Lin, X., Dreyer, C. A., Chen, X., Quinn, S. D., … Schlau-Cohen, G. S. (2022). Ligand-induced transmembrane conformational coupling in monomeric EGFR. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31299-z

Liu, S., Lin, X., & Zhang, B. (2021, November 18). Chromatin fiber breaks into clutches under tension and crowding (Vol. 11). Vol. 11. https://doi.org/10.1101/2021.11.16.468645

Lin, X., Leicher, R., Liu, S., & Zhang, B. (2021). Cooperative DNA looping by PRC2 complexes. Nucleic Acids Research, 49(11), 6238–6248. https://doi.org/10.1093/nar/gkab441

Oliveira Junior, A. B., Lin, X., Kulkarni, P., Onuchic, J. N., Roy, S., & Leite, V. B. P. (2021). Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms. Journal of Chemical Theory and Computation, 17(5), 3178–3187. https://doi.org/10.1021/acs.jctc.1c00027

Srinivasan, S., Regmi, R., Lin, X., Dreyer, C. A., Chen, X., Quinn, S. D., … Schlau-Cohen, G. S. (2021, October 28). Ligand-induced transmembrane conformational coupling in monomeric EGFR (Vol. 10). Vol. 10. https://doi.org/10.1101/2021.10.28.466294

Lin, X., Qi, Y., Latham, A. P., & Zhang, B. (2021). Multiscale modeling of genome organization with maximum entropy optimization. The Journal of Chemical Physics, 155(1), 010901. https://doi.org/10.1063/5.0044150

Lin, X., George, J. T., Schafer, N. P., Ng Chau, K., Birnbaum, M. E., Clementi, C., … Levine, H. (2021). Rapid assessment of T-cell receptor specificity of the immune repertoire. Nature Computational Science, 1(5), 362–373. https://doi.org/10.1038/s43588-021-00076-1

Rapid assessment of T-cell receptor specificity of the immune repertoire. (2021). Nature Computational Science. https://doi.org/10.1101/2020.04.06.028415

Ding, X., Lin, X., & Zhang, B. (2021). Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-21377-z

Guo, W.-H., Qi, X., Yu, X., Liu, Y., Chung, C.-I., Bai, F., … Wang, J. (2020). Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17997-6

Jin, S., Miller, M. D., Chen, M., Schafer, N. P., Lin, X., Chen, X., … Wolynes, P. G. (2020). Molecular-replacement phasing using predicted protein structures from <i>AWSEM-Suite. IUCrJ, 7(6), 1168–1178. https://doi.org/10.1107/S2052252520013494

Jin, S., Chen, M., Chen, X., Bueno, C., Lu, W., Schafer, N. P., … Wolynes, P. G. (2020). Protein Structure Prediction in CASP13 Using AWSEM-Suite. Journal of Chemical Theory and Computation, 16(6), 3977–3988. https://doi.org/10.1021/acs.jctc.0c00188

Chen, M., Chen, X., Jin, S., Lu, W., Lin, X., & Wolynes, P. G. (2020). Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The Journal of Physical Chemistry B, 124(48), 10889–10898. https://doi.org/10.1021/acs.jpcb.0c06719

Leicher, R., Ge, E. J., Lin, X., Reynolds, M. J., Xie, W., Walz, T., … Liu, S. (2020). 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. https://doi.org/10.1073/pnas.2003395117

Lin, X., Schafer, N. P., Lu, W., Jin, S., Chen, X., Chen, M., … Wolynes, P. G. (2019). Forging tools for refining predicted protein structures. Proceedings of the National Academy of Sciences, 116(19), 9400–9409. https://doi.org/10.1073/pnas.1900778116

Bhattacharya, S., & Lin, X. (2019). Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins. Biomolecules, 9(4), 146. https://doi.org/10.3390/biom9040146

Lin, X., Kulkarni, P., Bocci, F., Schafer, N., Roy, S., Tsai, M.-Y., … Jolly, M. (2019). Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules, 9(2), 77. https://doi.org/10.3390/biom9020077

Lin, X., Noel, J. K., Wang, Q., Ma, J., & Onuchic, J. N. (2018). 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). https://doi.org/10.1073/pnas.1805442115

Lin, X., Roy, S., Jolly, M. K., Bocci, F., Schafer, N. P., Tsai, M.-Y., … Onuchic, J. N. (2018). PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. Journal of Molecular Biology, 430(16), 2422–2438. https://doi.org/10.1016/j.jmb.2018.05.011

Lin, X., Roy, S., Jolly, M. K., Bocci, F., Schafer, N., Tsai, M.-Y., … Onuchic, J. N. (2018, February 14). PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer (Vol. 2). Vol. 2. https://doi.org/10.1101/264010

Chen, M., Lin, X., Lu, W., Schafer, N. P., Onuchic, J. N., & Wolynes, P. G. (2018). Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. Journal of Chemical Theory and Computation, 14(11), 6102–6116. https://doi.org/10.1021/acs.jctc.8b00683

Yao, X.-W., Wang, H., Liao, Z., Chen, M.-C., Pan, J., Li, J., … Suter, D. (2017). Quantum Image Processing and Its Application to Edge Detection: Theory and Experiment. Physical Review X, 7(3). https://doi.org/10.1103/PhysRevX.7.031041

Lin, X., Noel, J. K., Wang, Q., Ma, J., & Onuchic, J. N. (2016). 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. https://doi.org/10.1021/acs.jpcb.6b06775

Chen, M., Lin, X., Lu, W., Onuchic, J. N., & Wolynes, P. G. (2016). 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. https://doi.org/10.1021/acs.jpcb.6b09347

Chen, M., Lin, X., Zheng, W., Onuchic, J. N., & Wolynes, P. G. (2016). 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. https://doi.org/10.1021/acs.jpcb.6b02451

Lin, X., Eddy, N. R., Noel, J. K., Whitford, P. C., Wang, Q., Ma, J., & Onuchic, J. N. (2014). Order and disorder control the functional rearrangement of influenza hemagglutinin. Proceedings of the National Academy of Sciences, 111(33), 12049–12054. https://doi.org/10.1073/pnas.1412849111

Yao, X.-W., Chen, Z.-W., Mu, X.-Y., Pan, J., Yang, C., Lin, X.-C., … Wang, X.-W. (2010). Measurement method of logical gate in bulk spin quantum computer. Wuhan Ligong Daxue Xuebao/Journal of Wuhan University of Technology, 32(15), 142–145. https://doi.org/10.3963/j.issn.1671-4431.2010.15.034

Bi-Rong, Z., Qin, L., Xiao-Yang, M., Xing-Cheng, L., Chun, Y., Jian, P., & Zhong, C. (2010). Subspace quantum process tomography via nuclear magnetic resonance. Acta Physica Sinica, 59(10), 6837. https://doi.org/10.7498/aps.59.6837