LSL Suite S585
Development of advanced computational methods and their applications to the study of biomolecules and biomaterials.
Background and Training
- B.S. 1998, University of Science and Technology of China
- Ph.D. 2002, University of California at Irvine
Research in the Chen lab currently focuses on six key areas:
- Advanced sampling techniques and accurate implicit solvent models
- Intrinsically disordered proteins: structure, function and disease
- Multi-scale simulation of fibril growth and nucleation
- Gating and regulation of BK channels and TMEM16 family proteins
- Computational characterization and design of novel functional peptides
- Advanced software for molecular modeling of small angle scattering
X Liu and J. Chen, "Residual structures and transient long-range interactions of p53 transactivation domain: Assessment of explicit solvent protein force fields" J. Chem. Theory Comput. (in press) T. Le, Z. J
ia, S. C. Le, Y. Zhang, J. Chen and H. Yang, "An inner activation gate controls TMEM16F phospholipid scrambling", Nature Communications 10:1846 (2019).
Z. Jia, M. Yazdani, G. Zhang, J. Cui and J. Chen, "Hydrophobic gating in BK channels", Nature Communications 9:3408 | DOI: 10.1038/s41467-018-05970-3 (2018).
J. Chen and R. Kriwacki, "Intrinsically disordered proteins: structure, function and therapeutics", J. Mol. Biol. 430, 2275-77 (2018).
X. Liu and J. Chen, "HyRes: A coarse-grained model for multi-scale enhanced sampling of disordered protein conformations", Phys. Chem. Chem. Phys.19, 32421 - 32432 (2017).
Z. Jia, A. Beugelsdijk, J. Chen* and J. Schmit*, "The Levinthal Problem in Amyloid Aggregation: Sampling of a Flat Reaction Space" J. Phys. Chem. B 121, 1576-86 (2017)
K. H. Lee and J. Chen (2016), "Multiscale Enhanced Sampling of Intrinsically Disordered Protein Conformations" J. Comput. Chem. 37, 550-557
K. H. Lee and J. Chen (2017), "Re-balancing the GBMV implicit solvent protein force field for accurate simulation of protein conformational equilibra", J. of Comput. Chem. (in press).
K. H. Lee and J. Chen (2016), "Multiscale Enhanced Sampling of Intrinsically Disordered Protein Conformations" J. Comput. Chem. 37, 550-557.
Z. Jia, S. K. Whitaker, J. M. Tomich and J. Chen (2016), "Organization and structure of branched oligopeptide bilayers", Langmuir 32 (38), pp 9883–9891.
D. Ganguly and J. Chen (2015), "Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations" PLoS Comput. Biol. 11(4): e1004247.
W. Zhang and J. Chen (2014), "Accelerate sampling of atomistic energy landscapes using topology-based coarse-grained models" J. Chem. Theory Comput. 10, 918-923.
D. Ganguly, W. Zhang and J. Chen (2013), "Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins." PLoS Comput. Biol. 9(11): e1003363. doi:10.1371/journal.pcbi.1003363.
W. Zhang, D. Ganguly and J. Chen (2012). "Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins" PLoS Comput. Biol. 8(1): e1002353. doi:10.1371/journal.pcbi.1002353.
Y. Wang, J. C. Fisher, R. Matthew, L. Ou, S. Otieno, J. Sublett, L. Xiao, J. Chen, M. F. Roussel, and R. W. Kriwacki (2011). "Intrinsic Disorder Mediates the Diverse Cell Cycle Regulatory Functions of the Cyclin-dependent Kinase Inhibitor, p21Cip1", Nature Chem. Biol. 7, 214-221.