Chen Research Group
Computational Biochemistry & Biophysics

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At Kansas State University (since August 2007)
2014
47. J. Chen and J. M. Tomich (2014), "Free energy analysis of the conductance and charge selectivity of M2GlyR-derived channels", BBA - Biomembranes (in press) (Elsevier)
46. W. Zhang and J. Chen (2014), "Accelerate sampling of disordered protein conformations using replica exchange with guided annealing" J. Comput. Chem. (in press) (JCC)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)


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