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/

61 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
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  1
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  1
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  1
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  1
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  1
2020 Vo Q, Mahinthichaichan P, Shen J, Ellis C. How mu-Opioid Receptor Recognizes Fentanyl. Research Square. PMID 32935088 DOI: 10.21203/rs.3.rs-67888/v1  1
2020 Vo QN, Mahinthichaichan P, Shen J, Ellis CR. How -Opioid Receptor Recognizes Fentanyl. Biorxiv : the Preprint Server For Biology. PMID 32839778 DOI: 10.1101/2020.08.16.253013  1
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  1
2020 Mahinthichaichan P, Tsai CC, Payne GF, Shen J. Polyelectrolyte in Electric Field: Disparate Conformational Behavior along an Aminopolysaccharide Chain. Acs Omega. 5: 12016-12026. PMID 32548380 DOI: 10.1021/acsomega.0c00164  1
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  1
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  1
2019 Kim E, Li J, Kang M, Kelly DL, Chen S, Napolitano A, Panzella L, Shi X, Yan K, Wu S, Shen J, Bentley WE, Payne GF. Redox Is a Global Biodevice Information Processing Modality. Proceedings of the Ieee. Institute of Electrical and Electronics Engineers. 107: 1402-1424. PMID 32095023 DOI: 10.1109/JPROC.2019.2908582  1
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  1
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  1
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  1
2019 Li J, Wu S, Kim E, Yan K, Liu H, Liu C, Dong H, Qu X, Shi X, Shen J, Bentley WE, Payne GF. Electrobiofabrication: electrically-based fabrication with biologically-derived materials. Biofabrication. PMID 30759423 DOI: 10.1088/1758-5090/Ab06Ea  1
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  1
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  1
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  1
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  1
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  1
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  1
2017 Yan K, Liu Y, Zhang J, Correa SO, Shang W, Tsai CC, Bentley WE, Shen J, Scarcelli G, Raub CB, Shi XW, Payne GF. Electrical Programming of Soft Matter: Using Temporally Varying Electrical Inputs to Spatially Control Self Assembly. Biomacromolecules. PMID 29244943 DOI: 10.1021/Acs.Biomac.7B01464  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2016 Kim E, Liu Y, Ben-Yoav H, Winkler TE, Yan K, Shi X, Shen J, Kelly DL, Ghodssi R, Bentley WE, Payne GF. Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels. Advanced Healthcare Materials. PMID 27616350 DOI: 10.1002/Adhm.201600516  1
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  1
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  1
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  1
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  1
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  1
2015 Kim E, Xiong Y, Cheng Y, Wu HC, Liu Y, Morrow BH, Ben-Yoav H, Ghodssi R, Rubloff GW, Shen J, Bentley WE, Shi X, Payne GF. Chitosan to connect biology to electronics: Fabricating the bio-device interface and communicating across this interface Polymers. 7: 1-46. DOI: 10.3390/Polym7010001  1
2015 Yue Z, Shen J. Conformational Dynamics of Phus Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.2554  1
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  1
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  1
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  1
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  1
2014 Cote Y, Fu IW, Dobson ET, Goldberger JE, Nguyen HD, Shen JK. Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 118: 16272-16278. PMID 25089166 DOI: 10.1021/Jp5048024  1
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  1
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  1
2012 Wang Y, Shen JK, Schroeder SJ. Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits. The Journal of Physical Chemistry Letters. 3: 1007-10. PMID 26286564 DOI: 10.1021/jz3001882  1
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  1
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  1
2012 Du L, King JB, Morrow BH, Shen JK, Miller AN, Cichewicz RH. Diarylcyclopentendione metabolite obtained from a Preussia typharum isolate procured using an unconventional cultivation approach. Journal of Natural Products. 75: 1819-23. PMID 23046341 DOI: 10.1021/Np300473H  1
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  1
2012 Yi J, Morrow BH, Campbell AL, Shen JK, Richter-Addo GB. Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton. Chemical Communications (Cambridge, England). 48: 9041-3. PMID 22858591 DOI: 10.1039/C2Cc34655A  1
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  1
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  1
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  1
2011 Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MH, Shen JK, Warwicker J, Williams S, Word JM. Progress in the prediction of pKa values in proteins. Proteins. 79: 3260-75. PMID 22002859 DOI: 10.1002/Prot.23189  1
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  1
2011 Wang Y, Wallace JA, Koenig PH, Shen JK. Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model. Journal of Computational Chemistry. 32: 2348-58. PMID 21544841 DOI: 10.1002/jcc.21813  1
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  1
2010 Wallace JA, Shen JK. Probing the strand orientation and registry alignment in the propagation of amyloid fibrils. Biochemistry. 49: 5290-8. PMID 20491446 DOI: 10.1021/bi100137y  1
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  1
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  1
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