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Jana Shen, Ph.D - Publications

Affiliations: 
2007-2012 Department of Chemistry and Biochemistry University of Oklahoma, Norman, OK, United States 
 2012- Pharmaceutical Sciences University of Maryland School of Pharmacy 
Area:
Computational Chemistry and Biophysics, Drug and Material Design
Website:
https://www.computchem.org/
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60 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
2022 Henderson JA, Liu R, Harris JA, Huang Y, de Oliveira VM, Shen J. A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]. Living Journal of Computational Molecular Science. 4. PMID 36776714 DOI: 10.33011/livecoms.4.1.1563  0.485
2022 Martins de Oliveira V, Liu R, Shen J. Constant pH molecular dynamics simulations: Current status and recent applications. Current Opinion in Structural Biology. 77: 102498. PMID 36410222 DOI: 10.1016/j.sbi.2022.102498  0.433
2022 Harris JA, Liu R, Martins de Oliveira V, Vázquez-Montelongo EA, Henderson JA, Shen J. GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber. Journal of Chemical Theory and Computation. PMID 36377980 DOI: 10.1021/acs.jctc.2c00586  0.431
2021 Liu R, Verma N, Henderson JA, Zhan S, Shen J. Profiling MAP kinase cysteines for targeted covalent inhibitor design. Rsc Medicinal Chemistry. 13: 54-63. PMID 35224496 DOI: 10.1039/d1md00277e  0.327
2021 Henderson JA, Shen J. Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II. Journal of Chemical Information and Modeling. PMID 34964641 DOI: 10.1021/acs.jcim.1c01180  0.4
2021 Liu R, Zhan S, Che Y, Shen J. Reactivities of the Front Pocket N-Terminal Cap Cysteines in Human Kinases. Journal of Medicinal Chemistry. PMID 34647463 DOI: 10.1021/acs.jmedchem.1c01186  0.352
2021 Huang Y, Henderson JA, Shen J. Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2302: 275-287. PMID 33877633 DOI: 10.1007/978-1-0716-1394-8_15  0.458
2020 Ma S, Henderson JA, Shen J. Exploring the pH-Dependent Structure-Dynamics-Function Relationship of Human Renin. Journal of Chemical Information and Modeling. PMID 33356221 DOI: 10.1021/acs.jcim.0c01201  0.457
2020 Verma N, Henderson JA, Shen J. Proton-Coupled Conformational Activation of SARS Coronavirus Main Proteases and Opportunity for Designing Small-Molecule Broad-Spectrum Targeted Covalent Inhibitors. Journal of the American Chemical Society. PMID 33320670 DOI: 10.1021/jacs.0c10770  0.409
2020 Henderson JA, Huang Y, Beckstein O, Shen J. Alternative proton-binding site and long-distance coupling in sodium-proton antiporter NhaA. Proceedings of the National Academy of Sciences of the United States of America. PMID 32973095 DOI: 10.1073/pnas.2005467117  0.325
2020 Henderson JA, Verma N, Harris RC, Liu R, Shen J. Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors. The Journal of Chemical Physics. 153: 115101. PMID 32962355 DOI: 10.1063/5.0020458  0.531
2020 Henderson JA, Verma N, Shen J. Assessment of Proton-Coupled Conformational Dynamics of SARS and MERS Coronavirus Papain-like Proteases: Implication for Designing Broad-Spectrum Antiviral Inhibitors. Biorxiv : the Preprint Server For Biology. PMID 32637952 DOI: 10.1101/2020.06.30.181305  0.44
2020 Harris RC, Liu R, Shen J. Predicting Reactive Cysteines With Implicit-Solvent Based Continuous Constant pH Molecular Dynamics in Amber. Journal of Chemical Theory and Computation. PMID 32330035 DOI: 10.1021/Acs.Jctc.0C00258  0.533
2020 Wu S, Yan K, Li J, Huynh RN, Raub CB, Shen J, Shi X, Payne GF. Electrical cuing of chitosan's mesoscale organization Reactive & Functional Polymers. 148: 104492. DOI: 10.1016/J.Reactfunctpolym.2020.104492  0.3
2019 Harris RC, Shen J. GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations. Journal of Chemical Information and Modeling. PMID 31661616 DOI: 10.1021/Acs.Jcim.9B00754  0.538
2019 Tsai CC, Yue Z, Shen J. How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase. Journal of the American Chemical Society. PMID 31476863 DOI: 10.1021/Jacs.9B06064  0.748
2019 Liu R, Yue Z, Tsai CC, Shen J. Assessing Lysine and Cysteine Reactivities for Designing Targeted Covalent Kinase Inhibitors. Journal of the American Chemical Society. PMID 30945531 DOI: 10.1021/Jacs.8B13248  0.712
2019 Henderson JA, Shen J. Activation of the Voltage Gated Proton Channel Hv1: A Constant pH Molecular Dynamics Study Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.2345  0.429
2018 Henderson JA, Harris RC, Tsai CC, Shen J. How Ligand Protonation State Controls Water in Protein-Ligand Binding. The Journal of Physical Chemistry Letters. PMID 30188715 DOI: 10.1021/Acs.Jpclett.8B02440  0.422
2018 Huang Y, Harris R, Shen J. Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking, and Analysis. Journal of Chemical Information and Modeling. PMID 29949356 DOI: 10.1021/Acs.Jcim.8B00227  0.556
2018 Huang Y, Yue Z, Tsai CC, Henderson J, Shen J. Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships. The Journal of Physical Chemistry Letters. PMID 29461836 DOI: 10.1021/Acs.Jpclett.8B00238  0.743
2018 Yue Z, Shen J. pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL. Physical Chemistry Chemical Physics : Pccp. PMID 29336449 DOI: 10.1039/C7Cp08296G  0.755
2018 Tsai C, Payne GF, Shen J. Exploring pH-Responsive, Switchable Crosslinking Mechanisms for Programming Reconfigurable Hydrogels Based on Aminopolysaccharides Chemistry of Materials. 30: 8597-8605. DOI: 10.1021/Acs.Chemmater.8B03753  0.447
2018 Wu S, Yan K, Zhao Y, Tsai C, Shen J, Bentley WE, Chen Y, Deng H, Du Y, Payne GF, Shi X. Electrical Writing onto a Dynamically Responsive Polysaccharide Medium: Patterning Structure and Function into a Reconfigurable Medium Advanced Functional Materials. 28: 1803139. DOI: 10.1002/Adfm.201803139  0.306
2017 Yue Z, Chen W, Zgurskaya HI, Shen J. Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump. Journal of Chemical Theory and Computation. PMID 29117682 DOI: 10.1021/Acs.Jctc.7B00874  0.745
2017 Harris RC, Tsai CC, Ellis CR, Shen J. Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase. The Journal of Physical Chemistry Letters. PMID 28927275 DOI: 10.1021/Acs.Jpclett.7B02309  0.497
2017 Ellis CR, Tsai CC, Lin FY, Shen J. Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor. Journal of Computational Chemistry. PMID 28370344 DOI: 10.1002/Jcc.24719  0.546
2017 Deredge DJ, Huang W, Hui C, Matsumura H, Yue Z, Moënne-Loccoz P, Shen J, Wintrode PL, Wilks A. Ligand-induced allostery in the interaction of the Pseudomonas aeruginosa heme binding protein with heme oxygenase. Proceedings of the National Academy of Sciences of the United States of America. PMID 28289188 DOI: 10.1073/Pnas.1606931114  0.704
2017 Tsai C, Morrow BH, Chen W, Payne GF, Shen J. Toward Understanding the Environmental Control of Hydrogel Film Properties: How Salt Modulates the Flexibility of Chitosan Chains Macromolecules. 50: 5946-5952. DOI: 10.1021/Acs.Macromol.7B01116  0.421
2017 Beckstein O, Dotson DL, Coincon M, Huang Y, Lee C, Uzdavinys P, Nji E, Yashiro S, Chen W, Cameron AD, Shen J, Drew D. Molecular Mechanism of Electrogenic Sodium/Proton Antiport Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.1818  0.391
2017 Shen J. Atomic Insights into the pH-Induced Activation of Channels and Transporters Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.103  0.497
2016 Huang Y, Chen W, Wallace JA, Shen J. All-atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. Journal of Chemical Theory and Computation. PMID 27709966 DOI: 10.1021/Acs.Jctc.6B00552  0.523
2016 Huang Y, Chen W, Dotson DL, Beckstein O, Shen J. Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Nature Communications. 7: 12940. PMID 27708266 DOI: 10.1038/Ncomms12940  0.52
2016 Chen W, Huang Y, Shen J. Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics. The Journal of Physical Chemistry Letters. PMID 27648806 DOI: 10.1021/Acs.Jpclett.6B01853  0.528
2016 Ellis CR, Tsai CC, Hou X, Shen J. Constant pH Molecular Dynamics Reveals pH-modulated Binding of Two Small-molecule BACE1 Inhibitors. The Journal of Physical Chemistry Letters. PMID 26905811 DOI: 10.1021/Acs.Jpclett.6B00137  0.492
2015 Morrow BH, Payne GF, Shen J. pH-responsive self-assembly of polysaccharide through a rugged energy landscape. Journal of the American Chemical Society. PMID 26383701 DOI: 10.1021/Jacs.5B07761  0.423
2015 Chen W, Shi C, Shen J. Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts. Biophysical Journal. 109: 630-638. PMID 26244744 DOI: 10.1016/J.Bpj.2015.06.035  0.375
2015 Ellis CR, Shen J. pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition. Journal of the American Chemical Society. 137: 9543-6. PMID 26186663 DOI: 10.1021/Jacs.5B05891  0.524
2015 Chen W, Shi C, MacKerell AD, Shen J. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields. The Journal of Physical Chemistry. B. 119: 7902-10. PMID 26020564 DOI: 10.1021/Acs.Jpcb.5B02290  0.396
2015 Morrow BH, Payne GF, Shen JK. Titration Properties and pH-Dependent Aggregation of Chitosan Biophysical Journal. 108: 488a. DOI: 10.1016/J.Bpj.2014.11.2665  0.362
2015 Yue Z, Shen J. Conformational Dynamics of Phus Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.2554  0.726
2015 Chen W, Shen JK. Mechanism of Proton Transport of the M2 Proton Channel Studied by Constant pH Molecular Dynamics Biophysical Journal. 108: 439a. DOI: 10.1016/j.bpj.2014.11.2397  0.348
2015 Huang Y, Shen J. Towards the Mechanism of Sodium/Proton Antiporter in E. coli Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1679  0.521
2014 Chen W, Morrow BH, Shi C, Shen JK. Recent development and application of constant pH molecular dynamics. Molecular Simulation. 40: 830-838. PMID 25309035 DOI: 10.1080/08927022.2014.907492  0.391
2014 Morrow BH, Eike DM, Murch BP, Koenig PH, Shen JK. Predicting proton titration in cationic micelle and bilayer environments. The Journal of Chemical Physics. 141: 084714. PMID 25173037 DOI: 10.1063/1.4893439  0.391
2014 Chen W, Shen JK. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics. Journal of Computational Chemistry. 35: 1986-96. PMID 25142416 DOI: 10.1002/jcc.23713  0.414
2013 Morrow BH, Koenig PH, Shen JK. Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics. Langmuir : the Acs Journal of Surfaces and Colloids. 29: 14823-30. PMID 24215478 DOI: 10.1021/La403398N  0.384
2013 Chen W, Wallace JA, Yue Z, Shen JK. Introducing titratable water to all-atom molecular dynamics at constant pH. Biophysical Journal. 105: L15-7. PMID 23972860 DOI: 10.1016/J.Bpj.2013.06.036  0.748
2013 Morrow B, Koenig PH, Eike D, Shen JK. All Atom Molecular Dynamics Simulations of pH Dependent Surfactants Biophysical Journal. 104: 664a. DOI: 10.1016/J.Bpj.2012.11.3666  0.413
2013 Chen W, Wallace JA, Yue Z, Shen JK. Application of Explicit-Solvent Constant ph Molecular Dynamics to Proteins Biophysical Journal. 104: 508a. DOI: 10.1016/J.Bpj.2012.11.2803  0.756
2012 Morrow BH, Koenig PH, Shen JK. Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids. The Journal of Chemical Physics. 137: 194902. PMID 23181330 DOI: 10.1063/1.4766313  0.369
2012 Wallace JA, Shen JK. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH. The Journal of Chemical Physics. 137: 184105. PMID 23163362 DOI: 10.1063/1.4766352  0.396
2012 Wallace JA, Shen JK. Unraveling A Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins. The Journal of Physical Chemistry Letters. 3: 658-662. PMID 22866209 DOI: 10.1021/jz2016846  0.404
2012 Shi C, Wallace JA, Shen JK. Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation. Biophysical Journal. 102: 1590-7. PMID 22500759 DOI: 10.1016/j.bpj.2012.02.021  0.418
2011 Wallace JA, Shen JK. Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange. Journal of Chemical Theory and Computation. 7: 2617-29. PMID 26606635 DOI: 10.1021/ct200146j  0.479
2011 Morrow BH, Wang Y, Wallace JA, Koenig PH, Shen JK. Simulating pH titration of a single surfactant in ionic and nonionic surfactant micelles. The Journal of Physical Chemistry. B. 115: 14980-90. PMID 22050243 DOI: 10.1021/Jp2062404  0.386
2011 Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen BL, Xia K, Shen JK. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy. Proteins. 79: 3364-73. PMID 21748801 DOI: 10.1002/prot.23080  0.356
2010 Shen JK. Uncovering specific electrostatic interactions in the denatured states of proteins. Biophysical Journal. 99: 924-32. PMID 20682271 DOI: 10.1016/j.bpj.2010.05.009  0.336
2010 Shen JK. A method to determine residue-specific unfolded-state pKa values from analysis of stability changes in single mutant cycles. Journal of the American Chemical Society. 132: 7258-9. PMID 20446661 DOI: 10.1021/ja101761m  0.34
2009 Wallace JA, Shen JK. Predicting pKa values with continuous constant pH molecular dynamics. Methods in Enzymology. 466: 455-75. PMID 21609872 DOI: 10.1016/S0076-6879(09)66019-5  0.453
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