Chen Research Group
Computational Biochemistry & Biophysics

At University of Massachusetts, Amherst (since 01/2017)
62. X. Liu and J. Chen, "CG-IDP: A coarse-grained model for multi-scale enhanced sampling of disordered protein conformations" (submitted)
61. Q. Duan+, K. H. Lee+, C. Garcia, J. Chen, and W. Zhang, "MEFA (multiepitope fusion antigen) - Novel Technology for Structural Vaccinology, Proof from Computational and Empirical Immunogenicity Characterization of an Enterotoxigenic Escherichia coli (ETEC) Adhesin MEFA", J. Vaccines Vaccin, 8:367 (2017) (JVV)
60. X. Liu, Z. Jia and J. Chen, "Enhanced sampling of intrinsic structural heterogeneity of the BH3-only protein binding interface of Bcl-xL", J. Phys. Chem. B (under revision)
59. W. Zhang, S. C. HOwell, D. W. Wright, A. Heindel, X. Qiu, J. Chen* and J. E. Curtis*, "Combined Monte Carlo / Torsion-Angle Molecular Dynamics for Ensemble Modeling of Proteins, Nucleic Acids and Carbohydrates" J. Mol. Graph Model 73, 179-190 (2017) (JMGM)
58. K. H. Lee and J. Chen (2017), "Efficiency of Independent Sampling in Replica Exchange Simulations of Ordered and Disordered Proteins" J. Comput. Chem. (in press) (JCC)
57. 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) (ACS)
56. K. H. Lee and J. Chen*, "Re-balancing the GBMV implicit solvent protein force field for accurate simulation of protein conformational equilibra", J. Comput. Chem. 38, 1332-1341 (2017). (JCC)
At Kansas State University (since 08/2007)
55. S. J. Perkins, D. W. Wright, H. Zhang, E. H. Brookes, J. Chen, T. C. Irving, S. Krueger, D. J. Barlow, K. J. Edler, D. J. Scott, N. J. Terrill, S. M. King, P. D. Butler and J. E. Curtis, "Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)" J. Appl. Cryst. 49, 1861-75 (IUCR)
54. Z. Jia, S. K. Whitaker, J. M. Tomich and J. Chen (2016), "Organization and structure of branched oligopeptide bilayers", Langmuir 32, 9883-91 (ACS)
53. Z. Jia and J. Chen (2016), "Necessity of high-resolution for coarse-grained modeling of flexible proteins", J. Comput. Chem. 37, 1725-1733 (JCC)
52. K. H. Lee and J. Chen (2016), "Multiscale Enhanced Sampling of Intrinsically Disordered Protein Conformations" J. Comput. Chem. 37, 550-557 (JCC)
51. J. Chen (2015), "An Atomistic Glimpse of the Orderly Chaos of One Protein", Biophys. J. 109(8):1511-2 (Invited New & Notable article). (Cell)
50. X. Liu, A. Beugelsdijk and J. Chen (2015), "Dynamics of the BH3-only protein binding interface of Bcl-xl", Biophys. J. 109, 1049-57 (Cell)
49. 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 (PLoS)
48. H. Huang, D. Ganguly, J. Chen and X. S. Sun (2015), "Conformational Flexibility and pH Effects on Anisotropic Growth of Sheet-Like Assembly of Amphiphilic Peptides", J. Nanosci Nanotech 15, 4470-4479 (JNN)
47. J. Chen and J. M. Tomich (2014), "Free energy analysis of the conductance and charge selectivity of M2GlyR-derived channels", BBA - Biomembranes 1838, 2319-2325. (PubMed) (Elsevier)
46. W. Zhang and J. Chen (2014), "Replica exchange with guided annealing for accelerated sampling of disordered protein conformations" J. Comput. Chem. 35, 1682-1689. (JCC) (PubMed)
45. 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. (ACS)
44. P. Sukthankar, S. Gudlur, L. A. Avila, S. Whitaker, B. B. Katz, Y. Hiromasa, J. Gao, P. Thapa, D. Moore, T. Iwamoto, J. Chen, and J. M. Tomich (2013), "Branched-Oligopeptide Forms Capsules with Lipid Vesicle-Like Characteristics", Langmuir 29, 14648-14654. (ACS) (PubMed)
43. 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 (PLoS) (PubMed)
42. W. Zhang and J. Chen (2013), "Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions", J. Chem. Theory Comput. 9, 2849-2856. (ACS) (Access the recommendation on F1000Prime)
41. J. Gao and J. Chen (2013), "Effects of Flanking Loops on Membrane Insertion of Transmembrane Helices: A Role for Peptide Conformational Equilibrium" J. Phys. Chem. B, 117(28), 8330-8339. (ACS) (PubMed)
40. C. McDowell, J. Chen and J. Chen (2013), "Potential Conformational Heterogeneity of p53 bound to S100B(betabeta)", J. Mol. Biol. 425, 999-1010. (JMB) (PubMed)
39. S. Gudlur, X. Yao, J. Gao, M. Loeb, Y. Hiromasa, J. Chen, T. Iwamoto, and J. M. Tomich (2012). "Branched Amphipathic Peptides that Self-Assemble into Lipid-Free Bilayer Nanovesicles" PLoS ONE 7(9): e45374. (PLoS) (PubMed)
38. D. Ganguly, S. Otieno, B. Waddell, L. Iconaru, R. W. Kriwacki and J. Chen (2012). "Electrostatically Accelerated Coupled Binding and Folding of Intrinsically Disordered Proteins" J. Mol. Biol. 422, 674-84. (PubMed)
37. J. Chen (2012). "Towards the physical basis of how intrinsic disorder mediates protein function", Arch. Biochem. Biophys. 524, 123-131. (PubMed) (ScienceDirect)
36. 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 (PLoS) (PubMed)
35. U. Bukovnik, J. Gao, J., G.A. Cook1, L.P. Shank, M.B. Seabra, B.D. Schultz, T. Iwamoto, J. Chen and J.M. Tomich (2012). "Structural and biophysical properties of a synthetic channel-forming peptide: Designing a clinically relevant anion selective pore" BBA - Biomembranes 1818, 1039-1048. (ScienceDirect)
34. J. Chen, J. Cheng and A. K. Dunker (2012). "Intrinsically Disordered Proteins: Analysis, Prediction, Simulation, and Biology", Pac. Symp. Biocomput. 17, 67-69. (Editorial) (PSB Online)
33. D. Ganguly, W. Zhang and J. Chen (2012). "Synergetic folding of two intrinsically disordered proteins. Searching for conformational selection" Mol. BioSyst. 8, 198-209. (Front Cover) (PubMed) (RSC) (featured as the top 10% of the most highly cited articles published in Mol Biosyst in 2011-2012).
32. J. Chen and A. Zolkiewska (2011). "Force-Induced Unfolding Simulation of the Human Notch1 Negative Regulatory Region: Possible Roles of the Heterodimerization Domain in Mechanosensing" PLoS ONE 6(7): e22837. doi:10.1371/journal.pone.0022837 (PLoS) (PubMed)
31. 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. (PubMed) (Nature) (Nature News and Views) (K-State Today)
30. D. Ganguly and J. Chen (2011). "Topology-based modeling of intrinsically disordered proteins: balancing intrinsic structural propensities and intermolecular interactions" PROTEINS 79, 1251-1266. (PubMed) (PROTEINS)
29. T. H. Click, D. Ganguly and J. Chen (2010). "Intrinsically disordered proteins in a physics-based world", Int. J. Mol. Sci. 11, 5292-5309. (Invited Review) (MDPI) (PubMed)
28. J. Chen (2010). "Effective approximation of molecular volume using atom-centered dielectric functions in generalized Born" J. Chem. Theory Comput. 6, 2790-2803. (ACS)
27. A. I. Herrera, A. Al-Rawi, G. A. Cook, J. Gao, T. Iwamoto, O. Prakash. J. M. Tomich and J. Chen (2010). "Structural Characterization of Two Channel-Forming Peptides: Consequences of Introducing a C-Terminal Tryptophan". PROTEINS 78, 2238-2250. (PubMed) (PROTEINS)
26. M. Minchino, J. Chen, R. C. Stevens and C. L. Brooks III (2010). "FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A". PROTEINS 78, 2189-2201. (PubMed) (PROTEINS)
25. R. S. Armen, J. Chen and C. L. Brooks III (2009). "An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics". J. Chem. Theory Comput. 5, 2909-2923. (PubMed) (ACS)
24. D. Ganguly and J. Chen (2009). "Structural interpretation of paramagnetic relaxation enhancement-derived distances for disordered protein states". J. Mol. Biol. 390, 467-477. (PubMed)
23. D. Ganguly and J. Chen (2009). "Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding." J. Am. Chem. Soc. 131, 5214-5223. (PubMed) (ACS)
22. M. Taufer, R. S. Armen, J. Chen, P. J. Teller, and C. L. Brooks III (2009). "Computational multi-scale modeling in protein-ligand docking". IEEE Eng. Med. Biol. 28, 58-69. (PubMed)
21. J. Chen (2009). "Intrinsically Disordered p53 Extreme C-Terminus Binds to S100B(ββ) through “Fly-Casting”". J. Am. Chem. Soc. 131, 2088-2089. (PubMed) (ACS)
20. J. Lee, J. Chen, C. L. Brooks III and W. Im (2008). "Application of Solid-state NMR restraint potentials in membrane protein modeling". J. Magn. Reson. 193, 68-76. (PubMed) ( JMR Online)
19. J. Chen, C. L. Brooks III and Jana Khandogin (2008). "Recent advances in implicit solvent based methods for biomolecular simulations". Curr. Opin. Struct. Biol. 18, 140-148 (Invited Review). (PubMed)
At the Scripps Research Institute (2002-2007)
18. J. Chen and C. L. Brooks III (2008). "Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions". Phys. Chem. Chem. Phys. 10, 471-481 (Invited Article). (PubMed) (RSC)
17. J. Chen, C. L. Brooks III and H. A. Scheraga (2008). "Revisiting carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions and entropy". J. Phys. Chem. B 112, 242-249. (PubMed)
16. J. Chen and C. L. Brooks III (2007). "Critical importance of length scale dependence in implicit modeling of hydrophobic interactions". J. Am. Chem. Soc. 129, 2444-2445. (PubMed)
15. J. Chen and C. L. Brooks III (2007). "Can molecular dynamics simulations provide high-resolution refinement of protein structure?". PROTEINS 67, 922-930. (PubMed)
14. J. Khandogin, J. Chen and C. L. Brooks III (2006). "Exploring atomistic details of pH-dependent peptide folding". Proc. Natl. Acad. Sci. U. S. A. 103, 18546-18550. (PubMed)
13. J. Chen, W. Im and C. L. Brooks III (2006). "Balancing solvation and intramolecular interactions: Toward a consistent generalized Born force field". J. Am. Chem. Soc. 128, 3728-36. (PubMed)
12. J. Chen, W. Im and C. L. Brooks III (2005). "Application of torsion angle molecular dynamics for efficient sampling of protein conformation". J. Comput. Chem. 26, 1565-78. (PubMed)
11. W. Im, J. Chen and C. L. Brooks III (2005). "Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models". Adv. Protein Chem. 72, 173-198. (PubMed)
10. J. Chen, H. S. Won, W. Im, H. J. Dyson and C. L. Brooks III (2005). "Generation of native-like models from limited NMR Data, modern force field and advanced conformational sampling". J. Biomol. NMR. 31, 59-64. (PubMed)
9. J. Chen, W. Im and C. L. Brooks III (2004). "Refinement of NMR structures using implicit solvent and advanced sampling techniques". J. Am. Chem. Soc. 126, 16038-16047. (PubMed)
8. J. Chen, C. L. Brooks III and P. E. Wright (2004). "Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation". J. Biomol. NMR. 29, 243-257. (PubMed)
At the University of California at Irvine (1998-2002)
7. J. Chen, D. Nietlispach, V. A. Mandelshtam, and A. J. Shaka (2004). "Ultra-high resolution 3D NMR spectra from limited-size data sets". J. Magn. Reson. 169, 215-224. (PubMed)
6. A. Luchow, D. Neuhauser, J. Ka, R. Baer, J. Chen and V. A. Mandelshtam (2003). "Computing energy levels by inversion of imaginary-time cross-correlation functions". J. Phys. Chem. A. 107, 7175-7180. (ACS)
5. G. A. Armstrong, J. Chen, K. E. Cano, A. J. Shaka and V. A. Mandelshtam (2003). "Regularized resolvent transform for direct calculation of 45 degree projections of 2D J spectra". J. Magn. Reson. 164, 136-144. (PubMed)
4. J. Chen, A. A. De Angelis, V. A. Mandelshtam and A. J. Shaka (2003). "Progress on the two-dimensional filter diagonalization method. An efficient doubling scheme for two-dimensional constant-time NMR". J. Magn. Reson. 162, 74-89. (PubMed)
3. J. Chen, A. J. Shaka, V. A. Mandelshtam (2000). "RRT: the regularized resolvent transform for high-resolution spectral estimation". J. Magn. Reson. 147, 129-137. (PubMed)
2. J. Chen, V. A. Mandelshtam and A. J. Shaka (2000). "Regularization of the filter diagonalization method: FDM2K". J. Magn. Reson. 146, 363-368. (PubMed)
1. J. Chen and V. A. Mandelshtam (2000). "Multi-scale filter diagonalization method for spectral analysis of noisy data with nonlocalized features". J. Chem. Phys. 112, 4429-4437. (AIP)

| LSL S585 | IALS | Chemistry | Biochem & Mol Biol | UMass Amherst