Publications

[2026]$ Current Work

15bioRxiv

Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization

Y. Zhang^#, A. Sood^#, A. Athreya, and B. Zhang^*

bioRxiv, 2026 Preprint

14bioRxiv

MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations

S. Liu^#, Y. Zhang^#, I. Riveros, C. Wang, and B. Zhang^*

bioRxiv, 2026 Preprint

13JACS

A Glimpse into the Initial Microsecond of Biomolecular Condensation

L. Zhu^#, G. Liao^#, Y. Zhang^#, Y. Guo, J. Chen, S. Zhou, Z. Wu, Y. Huang, X. Lu, C. Chen, H. Chen, Y. Weng^*, and X. Zhang^*

Journal of the American Chemical Society, 2026 Published

12BOOK

Intrinsically Disordered Proteins

Y. Zhang^#, X. Liu^#, and J. Chen^*

In Generalized-Ensemble Algorithms: Ideas and Applications, Springer, 2026 In Press

[2025]$ Publications

11eLife

Protein Language Model Identifies Disordered, Conserved Motifs Implicated in Phase Separation

Y. Zhang, J. Zheng, and B. Zhang^*

eLife, 2025 Reviewed Preprint

10BIOC

Coarse-Grained Simulations of Phosphorylation Regulation of p53 Autoinhibition

S. Barethiya^#, S. Schultz^#, Y. Zhang, and J. Chen^*

Biochemistry 64(7), 1636, 2025 Published

09BPJ

Tracking Flaviviral Protease Conformational Dynamics by Tuning Single-Molecule Nanopore Tweezers

S. A. Shorkey^#, Y. Zhang^#, J. Sharp^#, S. Clingman, L. Nguyen, J. Chen^*, and M. Chen^*

Biophysical Journal 124(1), 145–157, 2025 Published

[2024]$ Publications

08JPCB

Likely Over-Stabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water

X. Gong^#, Y. Zhang^#, and J. Chen

Journal of Physical Chemistry B 128(47), 11554, 2024 Published

07BST

Backbone Interactions and Secondary Structures in Phase Separation of Disordered Proteins

S. Li, Y. Zhang, and J. Chen^*

Biochemical Society Transactions 52(1), 319–329, 2024 Published

06JACS

Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation

Y. Zhang^#, S. Li^#,*, X. Gong, and J. Chen^*

Journal of the American Chemical Society 146(1), 342–357, 2024 Published

[2023]$ Publications

05JCTC

Re-balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations

Y. Zhang, X. Liu^*, and J. Chen^*

Journal of Chemical Theory and Computation 19(5), 1602, 2023 Published

04FMB

Coupled Binding and Folding of Disordered SPIN N-terminal Region in Myeloperoxidase Inhibition

Y. Zhang^#, X. Liu^#, and J. Chen^*

Frontiers in Molecular Biosciences 10, 1130189, 2023 Published

[2022]$ Publications

03JCIM

Towards Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions

Y. Zhang, X. Liu^*, and J. Chen^*

Journal of Chemical Information and Modeling 62(18), 4523–4536, 2022 Published

02JMB

Intrinsically Disordered N-terminal Domain of p53 Interacts with Mitochondrial PTP Regulator Cyclophilin D

J. Zhao, X. Liu, A. Blayney, Y. Zhang, et al.

Journal of Molecular Biology 434(9), 167552, 2022 Published

[2021]$ Publications

01BIO

Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions