|
|
| |
|
At University of Massachusetts, Amherst (since 01/2017) |
| 2024 |
| 113. |
S. ZBarethiya#, S.Schultz#, Y. Zhang, and J. Chen, "Coarse-Grained
Simulations of Phosphorylation Regulation of p53 Autoinhibition"
(submitted)
| | 112. |
F. Tama* and J. Chen*, "Data Science for Integrated Dynamic
Structural Biology - the 21st IUPAB Congress Session Summary Commentary",
Biophysical Reviews (2024) (DOI: 10.1007/s12551-024-01222-5).
(Springer)
| | 111. |
X. Gong#, Y. Zhang#, and J. Chen, "Likely over-stabilization of
charge-charge interactions in CHARMM36m(w): a case for a99SB-disp
water" J. Phys. Chem. B (in press)
| | 110. |
S. P. Le, J. Krishna, P. Gupta, R. Dutta, S. Li, J. Chen*, and
S. Thayumanavan*, "Polymers for Disrupting Protein-Protein
Interactions - Where Are We and Where We Want to Be",
Biomacromolecus 25, 10, 6229 - 6249 (2024)
(ACS)
| | 109. |
E. B. Nordquist, Z. Jia, J. Chen, "Small molecule NS11021
promotes BK channel activation by increasing inner pore hydration"
J. Chem. Inf. Model 64, 19, 7616 - 7625 (2024).
(bioRxiv)
(ACS)
| | 108. |
Z. Jia#, G. Zhang#, J. Shi, J. Cui* and J. Chen*, "Intrinsic
Opening of BK Channels Derives from Inherent Leakage in Hydrophobic
Gating" (bioRxiv)
| | 107. |
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" (bioRxiv)
| | 106. |
Y. Zhang#, X. Liu# and J. Chen, "Intrinscially disordered proteins", in
"Generalized-Ensemble Algorithms - Ideas and Applications", Edited by Sugita
and Okomoto, Springer, 2024.
| | 105. |
V. Nguyen*, C. Özden*, K. Dong, A. Ocampo, N. Dziedzic, D. Flaherty, J. Huang,
D. Tomchick, J. Chen, S. Garman, M. Stratton, "A domain-swapped CaMKII conformation
facilitates linker-mediated allosteric regulation" (submitted)
(bioRxiv)
| | 104. |
V. Burtscher, J. Mount, J. Huang, J. Cowgill, Y. Chang, K. Bickel, J. Chen,
P. Yuan, and B. Chanda, "Structural Basis for Hyperpolarization-dependent Opening
of Human HCN1 Channel", Nature Communications, 15, 5216 (2024).
(Nature)
| | 103. |
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).
| | 102. |
J. Huang, A. Korsunsky, M. Yazdani* and J. Chen*, "Targeting TRP
Channels: Recent Advances in Structure, Ligand Binding and Molecular
Mechanisms" Front. Mol. Neurosci., 16:1334370.
doi: 10.3389/fnmol.2023.1334370 (2024). (invited review)
(Frontiers)
| | 101. |
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)
| | 2023 |
| 100. |
J. Huang and J. Chen, "Hydrophobic gating in bundle-crossing
ion channels: a case study of TRPV4", Communication Biology 6:1094 (2023)
(Nature)
| | 99. |
E. B. Nordquist#, G. Zhang#, S. Barethiya, N. Ji, K. M. White, L. Han, Z. Jia, J. Shi,
J. Cui, and J. Chen, "Incorporating physics to overcome data
scarcity in predictive modeling of protein function: a case study
of BK channels", PLoS Comput. Biol. 19(9):e1011460 (2023)
(PLoS)
| | 98. |
L. Zheng#, S. Barethiya#, E. B. Nordquist, and J. Chen, "Machine learning
generation of dynamic protein conformational ensembles", Molecules
28, 4047 (2023)
(MDPI)
| | 97. |
E. B. Nordquist, Z. Jia and J. Chen, "Inner pore hydration free energy controls
the activation of the big potassium channel and its mutants", Biophys. J.
7, 1158-1167 (2023)
(ScienceDirect)
(
Best of 2023 in Biophysical Journal)
| | 96. |
Y. Zhang, X. Liu and J. Chen, "Coupled bindibg and folding of
SPIN N-terminal region in myeloperoxidase inhibition",
Front. Mol. Biosci. 10:1130189. doi: 10.3389/fmolb.2023.1130189 (2023)
(Frontiers)
| | 95. |
Y. Zhang, X. Liu* and J. Chen*, "Re-balancing replica exchange with
solute tempering for sampling dynamic protein conformations",
J. Chem. Theory Comput. 19, 1602-1614 (2023)
(ACS)
| | 2022 |
| 94. |
E. B. Nordquist#, S. Schultz# and J. Chen, "Using metadynamics
to explore the free energy of dewetting in biologically relevant nanopores",
J. Phys. Chem. B. 126, 6428-6437 (2022)
(ACS)
| | 93. |
E. B. Nordquist, E. M. Clerico, J. Chen*, and L. M. Gierasch*,
"Computationally-aided modeling of Hsp70-client interactions: past,
present, and future", J. Phys. Chem. B. 126, 36, 6780-6791 (2022)
(ACS)
| | 92. |
Y. Zhang, X. Liu* and J. Chen*, "Towards Accurate Coarsed-Grained
Simulations of Disordered Proteins and Their Dynamic Interactions",
J. Chem. Inf. Model 62 (18), 4523-4536 (2022)
(ACS)
| | 91. |
Z. Jia#, J. Huang# and J. Chen, "Activation of TMEM16F by Inner Gate
Charged Mutations and Mechanisms of Phospholipid and Ion Permeation",
Biophys J 121(18), 3445-3457 (2022)
(BJ)
| | 90. |
G. Zhang#, X. Xu#, Z. Jia#, Y. Geng, H. Liang, J. Shi, M. Marras,
C. Abella, K. L. Magleby, J. R. Silva, J. Chen*, X. Zou*, and J. Cui*,
"An allosteric agonist activates BK channels by perturbing coupling
between Ca2+ binding and pore opening",
Nature Communications 13, 6784 (2022)
(Nature)
| | 89. |
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)
| | 2021 |
| 88. |
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)
| | 87. |
E. B. Nordquist, C. A. English, E. M. Clerico, W. Sherman, L. M. Gierasch
and J. Chen, "Physics-Based Modeling Provides Predictive Understanding of Selectively
Promiscuous Substrate Binding by Hsp70 Chaperones PLoS Comput Biol 17(11): e1009567
(PLoS)
| | 86. |
L. G. Schrag#, X. Liu#, I. Thevarajan#, O. Prakash, M. Zolkiewski, and J. Chen,
"Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of
the Intrinsically Disordered p53 Transactivation Domain", J. Mol. Boil.
433, 167048 (2021)
(bioRxiv)
(JMB)
| | 85. |
X. Liu, X. Gong and J. Chen, "Accelerating atomistic simulations of
proteins using multiscale enhanced sampling with independent tempering",
J. Comput. Chem. 42, 358-364 (2021)
(DOI)
| | 84. |
Zhao, J., A. Blayney, X. Liu, C. Yang, X. Liu, Y. Xiao, L. Gandy, M. Cosgrove,
S. Solmazh, Y. Zhang, D. Ban, C. P. Baines, J. Chen, S. N. Loh and C. Wang,
"EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction"
Nature Communications 12:986 (2021).
(Nature)
(ScienceDaily)
| | 83. |
Z. Jia and J. Chen, "Specific PIP2 Binding Promotes Calcium
Activation of TMEM16A Chloride Channels" Communcation Biology 4: 259 (2021)
(Nature)
| | 2020 |
| 82. |
M. Yazdani, Z. Jia and J. Chen, "Hydrophobic Dewetting In Gating
and Regulation of Transmembrane Protein Channels" J. Chem. Phys. 153, 110901 (2020).
(Invited Perspective Article)
(AIP)
| | 81. |
J. Chen, X. Liu and J. Chen, "Targeting intrinsically disordered
proteins through dynamic interactions" Biomolecules 10, 743 (2020). (Invited Review)
(MDPI)
| | 80. |
M. Woodward, E Ostrander, S.P. Jeong, X. Liu, B. Scott, M. Unger,
J. Chen, D. Venkataraman, E.P. Debold, "Shifting the gears of a
molecular motor using positional isomers of an abiotic energy source",
Biophys. J. 119, 567-580 (2020).
(BJ)
(UMass News)
| | 79. |
M. Yazdani#, G. Zhang#, Z. Jia#, J. Shi, J. Cui, and J. Chen,
"Nonspecific membrane interactions can modulate BK channel
activation" eLife 9:e55571 (2020).
(eLife)
(UMass News)
| | 78. |
Z. Jia, J. Schmit and J. Chen, "Amyloid assembly is dominated by
misregistered kinetic traps on an unbiased energy landscape",
Proc. Natl. Acad. Sci. U. S. A. 117 (19) 10322-10328 (2020).
(PNAS)
(EurekaAlert)
(ScienceDaily)
| | 77. |
T Fu, X Liu, H Gao, J Ward, X Liu, B Yin, Z Wang, Y Zhuo, J. Yang,
J Chen, D R Lovley, J Yao, "Bioinspired bio-voltage memristors",
Nature Communications 11, 1861 (2020).
(Nature)
| | 76. |
XM Liu, H. Gao, J. Ward, XR Liu, B. Yin, T. Fu, J. Chen, D. R. Lovley and J Yao,
"Power generation from ambient humidity using protein nanowires",
Nature 10.1038/s41586-020-2010-9 (2020).
(Nature)
(Science Daily)
(The Engineer)
(Popular Science)
| | 75. |
X. Li, K. H. Lee, J. Chen and M. Chen, "Different Anomeric Sugar
Bound States of Maltose Binding Protein Resolved by a Cytolysin A
Nanopore Tweezer." ACS Nano 14(2): 1727-1737 (2020).
(ACS)
| | 74. |
X. Liu and J. Chen, "Modulation of p53 Transactivation Domain
Conformations by Ligand Binding and Cancer-Associated Mutations",
Pac. Symp. Biocomput. 25:195-206 (2020).
(PSB 2020)
| | 73. |
T. M. Marchinko, C. Liang, S. Savinov, J. Chen, R. Vachet, "Structural
heterogeneity in the pre-amyloid oligomers of beta-2-microglobulin",
J. Mol. Biol. 432(2): 396-409 (2020).
(PubMed)
| | 2019 |
| 72. |
X. Gong, M. Chiricotto, X. Liu, E. B. Nordquist, M. Feig, C. L. Brooks III and J. Chen,
"Parallelization and CUDA implementation of the GBMV2/SA model",
J. Comput. Chem 41(8): 830-838 (2019).
(Wiley)
| | 71. |
C. Liang, S. Savinov, J. Fejzo, S. Eyles, and J. Chen, "Modulation of
Amyloid-beta42 Conformation by Small Molecules Through Non-Specific
Binding" J. Chem. Theory Comput. 15:5169-5174 (2019).
(PubMed)
(ACS)
| | 70. |
L. G. Schrag, X. L. Cao, H. Dembelea, X. L. Liu, Q. Al Souhail,
M. R. Kanost, J. Chen, H. Jiang and O. Prakash, "Expression and
characterization of Manduca sexta stress responsive peptide-1, an
inducer of antimicrobial peptide synthesis", Biochem Mol Biol
J. 4:42-52 (2019).
(SciencePG)
| | 69. |
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. 15, 708-4720 (2019).
(PubMed)
(ACS)
| | 68. |
S. C. Le, Z. Jia, J. Chen and H. Yang, "Molecular basis of
PIP2-dependent regulation of the Ca2+-activated chloride channel
TMEM16A" Nature Communications 10:3769 (2019).
(Nature)
| | 67. |
T. Le, Z. Jia, S. C. Le, Y. Zhang, J. Chen and H. Yang, "An
inner activation gate controls TMEM16F phospholipid
scrambling", Nature Communications 10:1846 (2019).
(Nature)
| | 66. |
X. Liu, J. Chen and J. Chen, "Residual structures accelerate
binding of intrinsically disordered ACTR by promoting efficient
folding upon encounter" J. Mol. Biol. 431:422-432 (2019).
(ScienceDirect)
| | 2018 |
| 65. |
J. Chen, X. Liu and J. Chen, "Atomistic Peptide Folding
Simulations Reveal Interplay of Entropy and Long-Range Interactions
in Folding Cooperativity",
Scientific Reports DOI: 10.1038/s41598-018-32028-7 (2018).
(Nature)
| | 64. |
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). (Nature)
(UMass News Release)
(ScienceDaily)
(MedicalXpress)
(Reliawire)
(Evolution News)
| | 63. |
J. Chen and R. Kriwacki, "Intrinsically disordered proteins: structure, function and therapeutics",
J. Mol. Biol. 430, 2275-77 (2018). (Special Issue Editorial Overview)
(ScienceDirect)
| | 2017 |
| 62. |
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).
(RSC)
| | 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 121, 9160-9168
(2017).
(ACS)
| | 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, "Efficiency of Independent Sampling in Replica
Exchange Simulations of Ordered and Disordered Proteins" J. Comput. Chem. (2017)
(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) |
| 2016 |
| 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 (2016), "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)
| | 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) (Top 25% most cited article
|
| 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 ÂFly-CastingÂ".
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)
|
|