|
At Kansas State University (since August 2007) |
|
| 2016 |
| 58. |
Z. Jia, A. Beugelsdijk, J. Schmit* and J. Chen*, "The Levinthal
Problem in Amyloid Aggregation: Sampling of a Flat Reaction Space"
(submitted)
|
| 57. |
K. H. Lee and J. Chen*, "Re-balancing the GBMV implicit solvent
protein force field for accurate simulation of protein
conformational equilibra" (submitted)
|
| 56. |
K. H. Lee and J. Chen (2016), "Efficiency of Gibbs Sampling in Replica
Exchange Simulations of Ordered and Disordered Proteins" (submitted)
|
| 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. (accepted)
|
| 54. |
Z. Jia, S. K. Whitaker, J. M. Tomich and J. Chen (2016),
"Organization and structure of branched oligopeptide bilayers",
Langmuir (accepted)
(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)
|
| 2015 |
| 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)
|
| 2014 |
| 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)
|
| 2013 |
| 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)
( )
|
| 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)
|
| 2012 |
| 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).
|
| 2011 |
| 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)
|
| 2010 |
| 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)
|
| 2009 |
| 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)
|
| 2008 |
| 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) |
| 2008 |
| 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)
|
| 2007 |
| 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)
|
| 2006 |
| 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)
|
| 2005 |
| 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)
|
| 2004 |
| 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) |
| 2004 |
| 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)
|
| 2003 |
| 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)
|
| 2000 |
| 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)
|