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Jianhan Chen, Ph.D. - Publications

Affiliations: 
2002 University of California, Irvine, Irvine, CA 
Area:
Physical Chemistry, Analytical Chemistry
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106 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Huang J, Korsunsky A, Yazdani M, Chen J. Targeting TRP channels: recent advances in structure, ligand binding, and molecular mechanisms. Frontiers in Molecular Neuroscience. 16: 1334370. PMID 38273937 DOI: 10.3389/fnmol.2023.1334370  0.301
2023 Nordquist E, Zhang G, Barethiya S, Ji N, White KM, Han L, Jia Z, Shi J, Cui J, Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels. Plos Computational Biology. 19: e1011460. PMID 37713443 DOI: 10.1371/journal.pcbi.1011460  0.796
2023 Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. Biorxiv : the Preprint Server For Biology. PMID 37662293 DOI: 10.1101/2023.08.22.554378  0.785
2023 Nordquist E, Zhang G, Barethiya S, Ji N, White KM, Han L, Jia Z, Shi J, Cui J, Chen J. Incorporating physics to overcome data scarcity in predictive modeling of protein function: a case study of BK channels. Biorxiv : the Preprint Server For Biology. PMID 37425916 DOI: 10.1101/2023.06.24.546384  0.796
2023 Zheng LE, Barethiya S, Nordquist E, Chen J. Machine Learning Generation of Dynamic Protein Conformational Ensembles. Molecules (Basel, Switzerland). 28. PMID 37241789 DOI: 10.3390/molecules28104047  0.792
2023 Zhang Y, Liu X, Chen J. Coupled binding and folding of disordered SPIN N-terminal region in myeloperoxidase inhibition. Frontiers in Molecular Biosciences. 10: 1130189. PMID 36845554 DOI: 10.3389/fmolb.2023.1130189  0.616
2023 Zhang Y, Liu X, Chen J. Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations. Journal of Chemical Theory and Computation. PMID 36791464 DOI: 10.1021/acs.jctc.2c01139  0.641
2023 Nordquist EB, Jia Z, Chen J. Inner pore hydration free energy controls the activation of big potassium channels. Biophysical Journal. PMID 36774534 DOI: 10.1016/j.bpj.2023.02.005  0.8
2022 Zhang G, Xu X, Jia Z, Geng Y, Liang H, Shi J, Marras M, Abella C, Magleby KL, Silva JR, Chen J, Zou X, Cui J. An allosteric modulator activates BK channels by perturbing coupling between Ca binding and pore opening. Nature Communications. 13: 6784. PMID 36351900 DOI: 10.1038/s41467-022-34359-6  0.718
2022 Zhang Y, Liu X, Chen J. Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions. Journal of Chemical Information and Modeling. PMID 36083825 DOI: 10.1021/acs.jcim.2c00974  0.677
2022 Nordquist EB, Clerico EM, Chen J, Gierasch LM. Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future. The Journal of Physical Chemistry. B. PMID 36040440 DOI: 10.1021/acs.jpcb.2c03806  0.79
2022 Nordquist EB, Schultz SA, Chen J. Using Metadynamics To Explore the Free Energy of Dewetting in Biologically Relevant Nanopores. The Journal of Physical Chemistry. B. 126: 6428-6437. PMID 35998613 DOI: 10.1021/acs.jpcb.2c04157  0.781
2022 Jia Z, Huang J, Chen J. Activation of TMEM16F by Inner Gate Charged Mutations and Possible Lipid/Ion Permeation Mechanisms. Biophysical Journal. PMID 35978550 DOI: 10.1016/j.bpj.2022.08.011  0.739
2022 Zhao J, Liu X, Blayney A, Zhang Y, Gandy L, Mirsky PO, Smith N, Zhang F, Linhardt RJ, Chen J, Baines C, Loh SN, Wang C. Intrinsically Disordered N-terminal Domain (NTD) of p53 Interacts with Mitochondrial PTP Regulator Cyclophilin D. Journal of Molecular Biology. 434: 167552. PMID 35341741 DOI: 10.1016/j.jmb.2022.167552  0.5
2021 Nordquist EB, English CA, Clerico EM, Sherman W, Gierasch LM, Chen J. Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. Plos Computational Biology. 17: e1009567. PMID 34735438 DOI: 10.1371/journal.pcbi.1009567  0.778
2021 Gong X, Zhang Y, Chen J. Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions. Biomolecules. 11. PMID 34680048 DOI: 10.3390/biom11101416  0.792
2021 Schrag LG, Liu X, Thevarajan I, Prakash O, Zolkiewski M, Chen J. Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain. Journal of Molecular Biology. 167048. PMID 33984364 DOI: 10.1016/j.jmb.2021.167048  0.486
2021 Jia Z, Chen J. Specific PIP binding promotes calcium activation of TMEM16A chloride channels. Communications Biology. 4: 259. PMID 33637964 DOI: 10.1038/s42003-021-01782-2  0.743
2021 Zhao J, Blayney A, Liu X, Gandy L, Jin W, Yan L, Ha JH, Canning AJ, Connelly M, Yang C, Liu X, Xiao Y, Cosgrove MS, Solmaz SR, Zhang Y, ... ... Chen J, et al. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction. Nature Communications. 12: 986. PMID 33579943 DOI: 10.1038/s41467-021-21258-5  0.461
2020 Liu X, Gong X, Chen J. Accelerating atomistic simulations of proteins using multiscale enhanced sampling with independent tempering. Journal of Computational Chemistry. PMID 33301208 DOI: 10.1002/jcc.26461  0.773
2020 Yazdani M, Jia Z, Chen J. Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels. The Journal of Chemical Physics. 153: 110901. PMID 32962356 DOI: 10.1063/5.0017537  0.797
2020 Jia Z, Yazdani M, Zhang G, Cui J, Chen J. Publisher Correction: Hydrophobic gating in BK channels. Nature Communications. 11: 4497. PMID 32883959 DOI: 10.1038/S41467-020-18517-2  0.769
2020 Yazdani M, Zhang G, Jia Z, Shi J, Cui J, Chen J. Aromatic interactions with membrane modulate human BK channel activation. Elife. 9. PMID 32597752 DOI: 10.7554/Elife.55571  0.789
2020 Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules. 10. PMID 32403216 DOI: 10.3390/biom10050743  0.542
2020 Jia Z, Schmit JD, Chen J. Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 32345723 DOI: 10.1073/Pnas.1911153117  0.737
2020 Fu T, Liu X, Gao H, Ward JE, Liu X, Yin B, Wang Z, Zhuo Y, Walker DJF, Joshua Yang J, Chen J, Lovley DR, Yao J. Bioinspired bio-voltage memristors. Nature Communications. 11: 1861. PMID 32313096 DOI: 10.1038/S41467-020-15759-Y  0.509
2020 Liu X, Gao H, Ward JE, Liu X, Yin B, Fu T, Chen J, Lovley DR, Yao J. Power generation from ambient humidity using protein nanowires. Nature. PMID 32066937 DOI: 10.1038/S41586-020-2010-9  0.484
2020 Li X, Lee KH, Shorkey S, Chen J, Chen M. Different Anomeric Sugar Bound States of MBP Resolved by a Cytolysin A Nanopore Tweezer. Acs Nano. PMID 31995359 DOI: 10.1021/Acsnano.9B07385  0.371
2020 Liu X, Chen J. Modulation of p53 Transactivation Domain Conformations by Ligand Binding and Cancer-Associated Mutations. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 25: 195-206. PMID 31797597  0.525
2020 Yazdani M, Zhang G, Jia Z, Shi J, Cui J, Chen J. Author response: Aromatic interactions with membrane modulate human BK channel activation Elife. DOI: 10.7554/Elife.55571.Sa2  0.325
2019 Schrag LG, Cao X, Dembele H, Liu X, Souhail QA, Kanost MR, Chen J, Jiang H, Prakash O. Expression and Characterization of Stress Responsive Peptide-1; an Inducer of Antimicrobial Peptide Synthesis. Biochemistry and Molecular Biology (New York, N.Y.). 4: 42-52. PMID 33241193 DOI: 10.11648/j.bmb.20190403.12  0.45
2019 Gong X, Chiricotto M, Liu X, Nordquist E, Feig M, Brooks CL, Chen J. Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. Journal of Computational Chemistry. PMID 31875339 DOI: 10.1002/Jcc.26133  0.769
2019 Le SC, Jia Z, Chen J, Yang H. Molecular basis of PIP-dependent regulation of the Ca-activated chloride channel TMEM16A. Nature Communications. 10: 3769. PMID 31434906 DOI: 10.1038/S41467-019-11784-8  0.749
2019 Liu X, Chen J. Residual structures and transient long-range interactions of p53 transactivation domain: Assessment of explicit solvent protein force fields. Journal of Chemical Theory and Computation. PMID 31241933 DOI: 10.1021/Acs.Jctc.9B00397  0.582
2019 Le T, Jia Z, Le SC, Zhang Y, Chen J, Yang H. An inner activation gate controls TMEM16F phospholipid scrambling. Nature Communications. 10: 1846. PMID 31015464 DOI: 10.1038/S41467-019-09778-7  0.74
2019 Liu X, Chen J, Chen J. Residual Structure Accelerates Binding of Intrinsically Disordered ACTR by Promoting Efficient Folding upon Encounter. Journal of Molecular Biology. 431: 422-432. PMID 30528464 DOI: 10.1016/J.Jmb.2018.12.001  0.587
2018 Chen J, Liu X, Chen J. Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity. Scientific Reports. 8: 13668. PMID 30209295 DOI: 10.1038/S41598-018-32028-7  0.586
2018 Jia Z, Yazdani M, Zhang G, Cui J, Chen J. Hydrophobic gating in BK channels. Nature Communications. 9: 3408. PMID 30143620 DOI: 10.1038/S41467-018-05970-3  0.793
2018 Chen J, Kriwacki RW. Intrinsically Disordered Proteins: Structure, Function and Therapeutics. Journal of Molecular Biology. PMID 29906412 DOI: 10.1016/J.Jmb.2018.06.012  0.313
2018 Jia Z, Zhang G, Yanzdani M, Cui J, Chen J. Gating of BK Channels: Roles of the C-LINKER and a Potential Hydrophobic Gate Biophysical Journal. 114: 545a-546a. DOI: 10.1016/J.Bpj.2017.11.2981  0.36
2017 Liu X, Chen J. HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations. Physical Chemistry Chemical Physics : Pccp. 19: 32421-32432. PMID 29186229 DOI: 10.1039/C7Cp06736D  0.61
2017 Liu X, Jia Z, Chen J. Enhanced Sampling of Intrinsic Structural Heterogeneity of the BH3-Only Protein Binding Interface of Bcl-xL. The Journal of Physical Chemistry. B. PMID 28903561 DOI: 10.1021/Acs.Jpcb.7B06768  0.784
2017 Lee KH, Chen J. Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria. Journal of Computational Chemistry. PMID 28397268 DOI: 10.1002/Jcc.24734  0.403
2017 Zhang W, Howell SC, Wright DW, Heindel A, Qiu X, Chen J, Curtis JE. Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates. Journal of Molecular Graphics & Modelling. 73: 179-190. PMID 28292714 DOI: 10.1016/J.Jmgm.2017.02.010  0.386
2017 Jia Z, Beugelsdijk A, Chen J, Schmit JD. The Levinthal Problem in Amyloid Aggregation: Sampling of a Flat Reaction Space. The Journal of Physical Chemistry. B. PMID 28129689 DOI: 10.1021/Acs.Jpcb.7B00253  0.732
2017 Jia Z, Chen J, Schmit JD. The Levinthal Problem in Amyloid Aggregation: Identification of Good Coordinates in a Flat Reaction Space Biophysical Journal. 112: 198a. DOI: 10.1016/J.Bpj.2016.11.1099  0.327
2016 Perkins SJ, Wright DW, Zhang H, Brookes EH, Chen J, Irving TC, Krueger S, Barlow DJ, Edler KJ, Scott DJ, Terrill NJ, King SM, Butler PD, Curtis JE. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Journal of Applied Crystallography. 49: 1861-1875. PMID 27980506 DOI: 10.1107/S160057671601517X  0.357
2016 Jia Z, Whitaker SK, Tomich JM, Chen J. Organization and Structure of Branched Amphipathic Oligopeptide bilayers. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 27584835 DOI: 10.1021/Acs.Langmuir.6B02421  0.714
2016 Jia Z, Chen J. Necessity of high-resolution for coarse-grained modeling of flexible proteins. Journal of Computational Chemistry. PMID 27130454 DOI: 10.1002/Jcc.24391  0.763
2016 Lee KH, Chen J. Multiscale enhanced sampling of intrinsically disordered protein conformations. Journal of Computational Chemistry. 37: 550-7. PMID 26052838 DOI: 10.1002/Jcc.23957  0.403
2015 Chen J. Atomistic Glimpse of the Orderly Chaos of One Protein. Biophysical Journal. 109: 1511-2. PMID 26488639 DOI: 10.1016/J.Bpj.2015.09.001  0.366
2015 Liu X, Beugelsdijk A, Chen J. Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL. Biophysical Journal. 109: 1049-57. PMID 26331262 DOI: 10.1016/J.Bpj.2015.07.043  0.579
2015 Ganguly D, Chen J. Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations. Plos Computational Biology. 11: e1004247. PMID 25897952 DOI: 10.1371/Journal.Pcbi.1004247  0.392
2015 Lee KH, Chen J. Refining Multi-Scale Enhanced Sampling for Simulating Disordered Protein Conformations Biophysical Journal. 108: 161a. DOI: 10.1016/J.Bpj.2014.11.890  0.398
2015 Jia Z, Chen J. Necessity of High Physical Resolution in the Development of Flexible Coarse-Grained Protein Models Biophysical Journal. 108: 161a. DOI: 10.1016/J.Bpj.2014.11.889  0.416
2014 Zhang W, Chen J. Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models. Journal of Chemical Theory and Computation. 10: 918-23. PMID 26580171 DOI: 10.1021/Ct500031V  0.34
2014 Zhang W, Chen J. Replica exchange with guided annealing for accelerated sampling of disordered protein conformations. Journal of Computational Chemistry. 35: 1682-9. PMID 24995857 DOI: 10.1002/Jcc.23675  0.389
2014 Chen J, Tomich JM. Free energy analysis of conductivity and charge selectivity of M2GlyR-derived synthetic channels. Biochimica Et Biophysica Acta. 1838: 2319-25. PMID 24582709 DOI: 10.1016/J.Bbamem.2014.02.016  0.392
2013 Zhang W, Chen J. Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions. Journal of Chemical Theory and Computation. 9: 2849-56. PMID 26583873 DOI: 10.1021/Ct400191B  0.351
2013 Ganguly D, Zhang W, Chen J. Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins. Plos Computational Biology. 9: e1003363. PMID 24278008 DOI: 10.1371/Journal.Pcbi.1003363  0.401
2013 Gao J, Chen J. Effects of flanking loops on membrane insertion of transmembrane helices: a role for peptide conformational equilibrium. The Journal of Physical Chemistry. B. 117: 8330-9. PMID 23786317 DOI: 10.1021/Jp402356C  0.325
2013 McDowell C, Chen J, Chen J. Potential conformational heterogeneity of p53 bound to S100B(ββ). Journal of Molecular Biology. 425: 999-1010. PMID 23313430 DOI: 10.1016/J.Jmb.2013.01.001  0.369
2012 Ganguly D, Otieno S, Waddell B, Iconaru L, Kriwacki RW, Chen J. Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins. Journal of Molecular Biology. 422: 674-84. PMID 22721951 DOI: 10.1016/J.Jmb.2012.06.019  0.381
2012 Chen J. Towards the physical basis of how intrinsic disorder mediates protein function. Archives of Biochemistry and Biophysics. 524: 123-31. PMID 22579883 DOI: 10.1016/J.Abb.2012.04.024  0.401
2012 Zhang W, Ganguly D, Chen J. Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. Plos Computational Biology. 8: e1002353. PMID 22253588 DOI: 10.1371/Journal.Pcbi.1002353  0.441
2012 Bukovnik U, Gao J, Cook GA, Shank LP, Seabra MB, Schultz BD, Iwamoto T, Chen J, Tomich JM. Structural and biophysical properties of a synthetic channel-forming peptide: designing a clinically relevant anion selective pore. Biochimica Et Biophysica Acta. 1818: 1039-48. PMID 21835162 DOI: 10.1016/J.Bbamem.2011.07.037  0.39
2012 Ganguly D, Zhang W, Chen J. Synergistic folding of two intrinsically disordered proteins: searching for conformational selection. Molecular Biosystems. 8: 198-209. PMID 21766125 DOI: 10.1039/C1Mb05156C  0.434
2011 Chen J, Zolkiewska A. Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing. Plos One. 6: e22837. PMID 21829530 DOI: 10.1371/Journal.Pone.0022837  0.353
2011 Wang Y, Fisher JC, Mathew R, Ou L, Otieno S, Sublet J, Xiao L, Chen J, Roussel MF, Kriwacki RW. Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21. Nature Chemical Biology. 7: 214-21. PMID 21358637 DOI: 10.1038/Nchembio.536  0.343
2011 Ganguly D, Chen J. Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions. Proteins. 79: 1251-66. PMID 21268115 DOI: 10.1002/Prot.22960  0.427
2011 Gao J, Tomich J, Chen J. Molecular Modeling and Simulation of a Synthetic Peptide Channel Biophysical Journal. 100: 87a. DOI: 10.1016/J.Bpj.2010.12.682  0.461
2011 Bukovnik U, Sala-Rabanal M, Nichols C, Schultz B, Chen J, Tomich J. Synthetic Peptide-Based Channels: Candidates for Treatments of Channelopathies Biophysical Journal. 100: 87a. DOI: 10.1016/J.Bpj.2010.12.681  0.375
2011 Ganguly D, Chen J. Synergistic Folding and Binding of Two Intrinsically Disordered Proteins Biophysical Journal. 100: 60a. DOI: 10.1016/J.Bpj.2010.12.526  0.362
2010 Chen J. Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models. Journal of Chemical Theory and Computation. 6: 2790-803. PMID 26616080 DOI: 10.1021/Ct100251Y  0.346
2010 Click TH, Ganguly D, Chen J. Intrinsically disordered proteins in a physics-based world. International Journal of Molecular Sciences. 11: 5292-309. PMID 21614208 DOI: 10.3390/Ijms11125292  0.418
2010 Herrera AI, Al-Rawi A, Cook GA, Gao J, Iwamoto T, Prakash O, Tomich JM, Chen J. Structural characterization of two pore-forming peptides: consequences of introducing a C-terminal tryptophan. Proteins. 78: 2238-50. PMID 20544961 DOI: 10.1002/Prot.22736  0.399
2010 Michino M, Chen J, Stevens RC, Brooks CL. FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins. 78: 2189-201. PMID 20544957 DOI: 10.1002/Prot.22731  0.516
2010 Ganguly D, Chen J. Concerted Involvement of Long-Range Electrostatic Interactions and Fly-Catsing in Recognition of Intrinsically Disordered Proteins Biophysical Journal. 98: 257a. DOI: 10.1016/J.Bpj.2009.12.1400  0.398
2009 Armen RS, Chen J, Brooks CL. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. Journal of Chemical Theory and Computation. 5: 2909-2923. PMID 20160879 DOI: 10.1021/Ct900262T  0.514
2009 Ganguly D, Chen J. Structural interpretation of paramagnetic relaxation enhancement-derived distances for disordered protein states. Journal of Molecular Biology. 390: 467-77. PMID 19447112 DOI: 10.1016/J.Jmb.2009.05.019  0.395
2009 Taufer M, Armen R, Chen J, Teller P, Brooks C. Computational multiscale modeling in protein - Ligand docking Ieee Engineering in Medicine and Biology Magazine. 28: 58-69. PMID 19349252 DOI: 10.1109/Memb.2009.931789  0.464
2009 Ganguly D, Chen J. Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding. Journal of the American Chemical Society. 131: 5214-23. PMID 19278259 DOI: 10.1021/Ja808999M  0.375
2009 Chen J. Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting". Journal of the American Chemical Society. 131: 2088-9. PMID 19216110 DOI: 10.1021/Ja809547P  0.414
2009 Armen RS, Chen J, Brooks CL. An evaluation of explicit receptor flexibility in molecular docking using molecular dynamics and torsion angle molecular dynamics Journal of Chemical Theory and Computation. 5: 2909-2923. DOI: 10.1021/ct900262t  0.401
2009 Al-Rawi AN, Urbanc B, Ganguly D, Rahman TS, Chen J, Tomich J. Molecular Dynamics Simulations of a Single 11-Residue Beta-Sheet Adhesive and its Assembly Biophysical Journal. 96: 75a-76a. DOI: 10.1016/J.Bpj.2008.12.290  0.331
2009 Ganguly D, Chen J. Effects of Phosphorylation on the unbound states of an intrinsically disordered protein: A Computational Approach Biophysical Journal. 96: 320a. DOI: 10.1016/J.Bpj.2008.12.1604  0.388
2008 Lee J, Chen J, Brooks CL, Im W. Application of solid-state NMR restraint potentials in membrane protein modeling. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 193: 68-76. PMID 18462966 DOI: 10.1016/J.Jmr.2008.04.023  0.671
2008 Chen J, Brooks CL, Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Current Opinion in Structural Biology. 18: 140-8. PMID 18304802 DOI: 10.1016/J.Sbi.2008.01.003  0.569
2008 Chen J, Brooks CL. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Physical Chemistry Chemical Physics : Pccp. 10: 471-81. PMID 18183310 DOI: 10.1039/B714141F  0.579
2008 Chen J, Brooks CL, Scheraga HA. Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. The Journal of Physical Chemistry. B. 112: 242-9. PMID 17880128 DOI: 10.1021/Jp074355H  0.52
2007 Chen J, Brooks CL. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins. 67: 922-30. PMID 17373704 DOI: 10.1002/Prot.21345  0.556
2007 Chen J, Brooks CL. Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. Journal of the American Chemical Society. 129: 2444-5. PMID 17288425 DOI: 10.1021/Ja068383+  0.56
2006 Khandogin J, Chen J, Brooks CL. Exploring atomistic details of pH-dependent peptide folding. Proceedings of the National Academy of Sciences of the United States of America. 103: 18546-50. PMID 17116871 DOI: 10.1073/Pnas.0605216103  0.518
2006 Chen J, Im W, Brooks CL. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. Journal of the American Chemical Society. 128: 3728-36. PMID 16536547 DOI: 10.1021/Ja057216R  0.546
2005 Im W, Chen J, Brooks CL. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Advances in Protein Chemistry. 72: 173-98. PMID 16581377 DOI: 10.1016/S0065-3233(05)72007-6  0.508
2005 Chen J, Im W, Brooks CL. Application of torsion angle molecular dynamics for efficient sampling of protein conformations. Journal of Computational Chemistry. 26: 1565-78. PMID 16145655 DOI: 10.1002/Jcc.20293  0.562
2005 Chen J, Won HS, Im W, Dyson HJ, Brooks CL. Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. Journal of Biomolecular Nmr. 31: 59-64. PMID 15692739 DOI: 10.1007/S10858-004-6056-Z  0.538
2004 Chen J, Im W, Brooks CL. Refinement of NMR structures using implicit solvent and advanced sampling techniques. Journal of the American Chemical Society. 126: 16038-47. PMID 15584737 DOI: 10.1021/Ja047624F  0.541
2004 Chen J, Nietlispach D, Shaka AJ, Mandelshtam VA. Ultra-high resolution 3D NMR spectra from limited-size data sets. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 169: 215-24. PMID 15261616 DOI: 10.1016/J.Jmr.2004.04.017  0.591
2004 Chen J, Brooks CL, Wright PE. Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. Journal of Biomolecular Nmr. 29: 243-57. PMID 15213423 DOI: 10.1023/B:Jnmr.0000032504.70912.58  0.515
2003 Armstrong GS, Chen J, Cano KE, Shaka AJ, Mandelshtam VA. Regularized resolvent transform for direct calculation of 45 degrees projections of 2D J spectra. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 164: 136-44. PMID 12932465 DOI: 10.1016/S1090-7807(03)00129-0  0.707
2003 Chen J, De Angelis AA, Mandelshtam VA, Shaka AJ. Progress on the two-dimensional filter diagonalization method. An efficient doubling scheme for two-dimensional constant-time NMR. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 162: 74-89. PMID 12762985 DOI: 10.1016/S1090-7807(03)00045-4  0.587
2003 Lüchow A, Neuhauser D, Ka J, Baer R, Chen J, Mandelshtam VA. Computing energy levels by inversion of imaginary-time cross-correlation functions Journal of Physical Chemistry A. 107: 7175-7180. DOI: 10.1021/Jp034381P  0.601
2000 Chen J, Shaka AJ, Mandelshtam VA. RRT: the regularized resolvent transform for high-resolution spectral estimation Journal of Magnetic Resonance (San Diego, Calif. : 1997). 147: 129-37. PMID 11042056 DOI: 10.1006/Jmre.2000.2176  0.575
2000 Chen J, Mandelshtam VA, Shaka AJ. Regularization of the two-dimensional filter diagonalization method: FDM2K Journal of Magnetic Resonance (San Diego, Calif. : 1997). 146: 363-8. PMID 11001852 DOI: 10.1006/Jmre.2000.2155  0.578
2000 Chen J, Mandelshtam VA. Multiscale filter diagonalization method for spectral analysis of noisy data with nonlocalized features Journal of Chemical Physics. 112: 4429-4437. DOI: 10.1063/1.481005  0.584
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