Fruits

[12]. Y. Zhang, J. Zheng, B. Zhang*, “Protein Language Model Identifies Disordered, Conserved Motifs Driving Phase separation.” (Submitted)

[11] Y. Zhang#, X. Liu# and J. Chen, “Intrinsically disordered proteins”, in “Generalized-Ensemble Algorithms - Ideas and Applications”, Edited by Sugita and Okomoto, Springer, 2024. (Submitted to Springer)

[10] S. Barethiya#, S. Schultz#, Y. Zhang, J. Chen, “Coarse-Grained Simulations of Phosphorylation Regulation of p53 Autoinhibition.” (Submitted to Biochemistry)

[9] S. A. Shorkey#, Y. Zhang#, J. Sharp#, S. Clingman, L. Nguyen, J. Chen* and M. Chen, “Tuning single-molecule ClyA nanopore tweezers for real-time tracking of flaviviral protease conformational dynamics.”, *Biophys J. (2024). ScienceDirect

[8] X. Gong#, Y. Zhang#, J. Chen. “Likely Over-Stabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.”, J. Phys. Chem. B. (2024). ACS

[7] S. Li, Y. Zhang and J. Chen, “Protein Backbone Interactions and Secondary Structures in Biomolecular Phase Separation”, Biochem. Soc. Trans., BST20230618 (2024). (invited review) Portland Press

[6] Y. Zhang#, S. Li#,, X. Gong and J. Chen, “Toward Accurate Simulations of Coupling between Protein Secondary Structure and Phase Separation”, J. Am. Chem. Soc. 146, 342-357 (2024). ACS, UMass News, Phys.Org

[5] Y. Zhang, X. Liu* and J. Chen*, “Re-balancing replica exchange with solute tempering for sampling dynamic protein conformations”, J. Chem. Theory Comput. (2023). ACS

[4] Y. Zhang, X. Liu and J. Chen, “Coupled binding and folding of SPIN N-terminal region in myeloperoxidase inhibition”, Front. Mol. Biosci. (2023). Frontiers

[3] Y. Zhang, X. Liu* and J. Chen*, “Towards Accurate Coarsed-Grained Simulations of Disordered Proteins and Their Dynamic Interactions”, J. Chem. Inf. Model (2022). ACS

[2] J. Zhao, X. Liu, A. Blayney, Y. Zhang, L. Gandy, F. Zhang, R. J. Linhardt, J. Chen, C. Baines, S. N. Loh and C. Wang, “Intrinsically disordered N-terminal domain (NTD) of p53 interacts with mitochondrial PTP regulator Cyclophilin D” J. Mol. Biol. 434, 167552 (2022). JMB

[1] X. Gong#, Y. Zhang# and J. Chen, “Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions” Biomolecules, 11, 1416 (2021) (Invited Review). MDPI