Jana K. Shen

发表

Effects of system net charge and electrostatic truncation on all‐atom constant pH molecular dynamics

Wei Chen, Jana K. Shen, Wei Chen, 2014, J. Comput. Chem..

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit‐solvent model

Yuhang Wang, Jana K. Shen, Peter H. Koenig, 2011, J. Comput. Chem..

Reactivities of the Front Pocket N-Cap Cysteines in Human Kinases

Jana K. Shen, Ruibin Liu, Shaoqi Zhan, 2021, bioRxiv.

Progress in the prediction of pKa values in proteins

Sarah L. Williams, Jana K. Shen, J. Warwicker, 2011, Proteins.

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

Jana K. Shen, Yandong Huang, Wei Chen, 2016, Journal of chemical theory and computation.

Electrical Writing onto a Dynamically Responsive Polysaccharide Medium: Patterning Structure and Function into a Reconfigurable Medium

Gregory F. Payne, Xiaowen Shi, William E. Bentley, 2018, Advanced Functional Materials.

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange.

Jana K. Shen, J. A. Wallace, Jason A Wallace, 2011, Journal of chemical theory and computation.

A method to determine residue-specific unfolded-state pKa values from analysis of stability changes in single mutant cycles.

Jana K. Shen, 2010, Journal of the American Chemical Society.

Polyelectrolyte in Electric Field: Disparate Conformational Behavior along an Aminopolysaccharide Chain

Jana K. Shen, G. Payne, P. Mahinthichaichan, 2020, ACS omega.

Predicting pKa values with continuous constant pH molecular dynamics.

Jana K. Shen, J. A. Wallace, Jason A Wallace, 2009, Methods in enzymology.

Uncovering specific electrostatic interactions in the denatured states of proteins.

Jana K. Shen, Jana K Shen, 2010, Biophysical journal.

PROGRESS IN THE PREDICTION OF pK a VALUES IN PROTEINS

Nathan A. Baker, Emil Alexov, Damien Farrell, 2011 .

Chitosan to Connect Biology to Electronics: Fabricating the Bio-Device Interface and Communicating Across This Interface

Yi Liu, Gregory F. Payne, Yuan Xiong, 2014 .

GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations

Robert C. Harris, Jana K. Shen, Yandong Huang, 2019, J. Chem. Inf. Model..

Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation.

Jana K. Shen, Chuanyin Shi, J. A. Wallace, 2012, Biophysical journal.

Predicting proton titration in cationic micelle and bilayer environments.

Jana K. Shen, Peter H. Koenig, David M. Eike, 2014, The Journal of chemical physics.

Toward Understanding the Environmental Control of Hydrogel Film Properties: How Salt Modulates the Flexibility of Chitosan Chains

Jana K. Shen, G. Payne, Wei Chen, 2017 .

How μ-Opioid Receptor Recognizes Fentanyl

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2020, Research square.

How μ-Opioid Receptor Recognizes Fentanyl

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2020, bioRxiv.

Assessing Lysine and Cysteine Reactivities for Designing Targeted Covalent Kinase Inhibitors.

Jana K. Shen, Ruibin Liu, Cheng-Chieh Tsai, 2019, Journal of the American Chemical Society.

Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors

Robert C. Harris, Jana K. Shen, Jack A. Henderson, 2020, The Journal of chemical physics.

Diarylcyclopentendione metabolite obtained from a Preussia typharum isolate procured using an unconventional cultivation approach.

Jana K. Shen, A. Miller, R. Cichewicz, 2012, Journal of natural products.

GPU-Accelerated All-atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber

Jana K. Shen, Jack A. Henderson, Ruibin Liu, 2022, bioRxiv.

How μ-Opioid Receptor Recognizes Fentanyl

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2020, Research square.

A Proof-of-Concept Inhibitor of Endothelial Lipase Suppresses Triple-Negative Breast Cancer Cells by Hijacking the Mitochondrial Function

Jana K. Shen, Qun Zhou, Yuan Yao, 2022, Cancers.

Ligand-induced allostery in the interaction of the Pseudomonas aeruginosa heme binding protein with heme oxygenase

Jana K. Shen, P. Wintrode, A. Wilks, 2017, Proceedings of the National Academy of Sciences.

Electrical cuing of chitosan's mesoscale organization

Jana K. Shen, G. Payne, Xiaowen Shi, 2020 .

Continuous constant pH Molecular Dynamics Simulations of Transmembrane Proteins

Jana K. Shen, Jack A. Henderson, Yandong Huang, 2020, bioRxiv.

Electrobiofabrication: electrically based fabrication with biologically derived materials

Si Wu, Hua Dong, Changsheng Liu, 2019, Biofabrication.

Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships.

Jana K. Shen, Jack A. Henderson, Yandong Huang, 2018, The journal of physical chemistry letters.

Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels

Yi Liu, Kun Yan, Xiaowen Shi, 2016, Advanced healthcare materials.

pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape.

Gregory F Payne, Jana K. Shen, Jana Shen, 2015, Journal of the American Chemical Society.

Redox Is a Global Biodevice Information Processing Modality

Si Wu, Shuo Chen, Gregory F. Payne, 2019, Proceedings of the IEEE.

Exploring pH-Responsive, Switchable Crosslinking Mechanisms for Programming Reconfigurable Hydrogels Based on Aminopolysaccharides

Jana K. Shen, G. Payne, Cheng-Chieh Tsai, 2018, Chemistry of Materials.

Simulating pH titration of a single surfactant in ionic and nonionic surfactant micelles.

Jana K. Shen, Peter H. Koenig, J. A. Wallace, 2011, The journal of physical chemistry. B.

Probing the strand orientation and registry alignment in the propagation of amyloid fibrils.

Jana K. Shen, J. A. Wallace, Jason A Wallace, 2010, Biochemistry.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump.

Jana K. Shen, H. Zgurskaya, Wei Chen, 2017, Journal of chemical theory and computation.

Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.

Jana K. Shen, Peter H. Koenig, Jana K Shen, 2013, Langmuir : the ACS journal of surfaces and colloids.

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.

Jana K. Shen, Peter H. Koenig, Jana K Shen, 2012, The Journal of chemical physics.

Recent development and application of constant pH molecular dynamics

Wei Chen, Jana K. Shen, Chuanyin Shi, 2014, Molecular simulation.

How μ-opioid receptor recognizes fentanyl

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2021, Nature Communications.

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

Yandong Huang, Oliver Beckstein, Wei Chen, 2016, Nature Communications.

Alternative proton-binding site and long-distance coupling in Escherichia coli sodium–proton antiporter NhaA

Jana K. Shen, Jack A. Henderson, Yandong Huang, 2020, Proceedings of the National Academy of Sciences.

Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2023, bioRxiv.

Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits.

Jana K. Shen, S. Schroeder, Yuhang Wang, 2012, The journal of physical chemistry letters.

Introducing titratable water to all-atom molecular dynamics at constant pH.

Wei Chen, Zhi Yue, Jana K. Shen, 2013, Biophysical journal.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

Jana K. Shen, J. A. Wallace, Jason A Wallace, 2012, The Journal of chemical physics.

How Ligand Protonation State Controls Water in Protein-Ligand Binding.

Robert C. Harris, Jana K. Shen, Jack A. Henderson, 2018, The journal of physical chemistry letters.

Kinetics and Mechanism of Fentanyl Dissociation from the μ-Opioid Receptor

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2021, JACS Au.

Reactivities of the Front Pocket N-Terminal Cap Cysteines in Human Kinases.

Jana K. Shen, Ruibin Liu, Shaoqi Zhan, 2021, Journal of medicinal chemistry.

Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases

Jana K. Shen, Ruibin Liu, Shaoqi Zhan, 2023, J. Chem. Inf. Model..

Predicting Reactive Cysteines With Implicit-Solvent Based Continuous Constant pH Molecular Dynamics in Amber.

Robert C. Harris, Jana K. Shen, Ruibin Liu, 2020, Journal of chemical theory and computation.

Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis

Robert C. Harris, Robert C Harris, Jana K. Shen, 2018, J. Chem. Inf. Model..

Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II

Jana K. Shen, Jack A. Henderson, 2021, J. Chem. Inf. Model..

Conformational dynamics of cathepsin D and binding to a small‐molecule BACE1 inhibitor

Cheng-Chieh Tsai, Fang-Yu Lin, Jana Shen, 2017, J. Comput. Chem..

pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition.

Christopher R. Ellis, Jana K. Shen, Jana Shen, 2015, Journal of the American Chemical Society.

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

Jana K. Shen, Chuanyin Shi, J. A. Wallace, 2011, Proteins.

How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase.

Jana K. Shen, Cheng-Chieh Tsai, Z. Yue, 2019, Journal of the American Chemical Society.

Electro-Biofabrication. Coupling Electrochemical and Biomolecular Methods to Create Functional Bio-Based Hydrogels.

Jana K. Shen, W. Bentley, Eunkyoung Kim, 2023, Biomacromolecules.

Electrical Programming of Soft Matter: Using Temporally Varying Electrical Inputs To Spatially Control Self Assembly.

Giuliano Scarcelli, Gregory F Payne, William E Bentley, 2017, Biomacromolecules.

Mechanism of pH sensing in the human voltage-gated proton channel hHv1

Jana K. Shen, Yandong Huang, Zhitao Cai, 2022, bioRxiv.

Proton-Coupled Conformational Activation of SARS Coronavirus Main Proteases and Opportunity for Designing Small-Molecule Broad-Spectrum Targeted Covalent Inhibitors

Jana K. Shen, Jack A. Henderson, N. Verma, 2020, Journal of the American Chemical Society.

Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors.

Christopher R. Ellis, Jana K. Shen, Jana Shen, 2016, The journal of physical chemistry letters.

Kinetics and Mechanism of Fentanyl Dissociation from the µ-Opioid Receptor

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2021 .

Profiling MAP kinase cysteines for targeted covalent inhibitor design.

Jana K. Shen, Jack A. Henderson, Ruibin Liu, 2022, RSC medicinal chemistry.

Exploring the pH-dependent structure-dynamics-function relationship of human renin

Jana K. Shen, Shuhua Ma, Jana Shen, 2020, bioRxiv.

Zooming in on a small multidrug transporter reveals details of asymmetric protonation

Jana K. Shen, 2018, Proceedings of the National Academy of Sciences.

Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts

Wei Chen, Jana K. Shen, Jana Shen, 2015, Biophysical journal.

Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads.

Jana K. Shen, Shuhua Ma, Ruibin Liu, 2023, Journal of chemical information and modeling.

Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

Alexander D. MacKerell, Jana K. Shen, Chuanyin Shi, 2015, The journal of physical chemistry. B.

Constant pH molecular dynamics simulations: Current status and recent applications.

Jana K. Shen, Ruibin Liu, Vinícius Martins de Oliveira, 2022, Current opinion in structural biology.

Unraveling A Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins.

Jana K. Shen, J. A. Wallace, Jason A Wallace, 2012, The journal of physical chemistry letters.

H172Y mutation perturbs the S1 pocket and nirmatrelvir binding of SARS-CoV-2 main protease through a nonnative hydrogen bond

Jana K. Shen, R. Hilgenfeld, Xinyuanyuan Sun, 2022, Research square.

A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0].

Jana K. Shen, Jack A. Henderson, Ruibin Liu, 2022, Living journal of computational molecular science.

Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease

Jana K. Shen, Mingzhe Shen, P. Mahinthichaichan, 2023, J. Chem. Inf. Model..

Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin

Jana K. Shen, G. Payne, Aarion Romany, 2023, bioRxiv.

Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines

Jana K. Shen, Mingzhe Shen, Ruibin Liu, 2023, bioRxiv.

Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis

Christopher R. Ellis, Jana K. Shen, P. Mahinthichaichan, 2023, J. Chem. Inf. Model..

An Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease

Jana K. Shen, Mingzhe Shen, P. Mahinthichaichan, 2023, bioRxiv.

Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles

Jana K. Shen, H. Nguyen, J. Goldberger, 2014, The journal of physical chemistry. C, Nanomaterials and interfaces.

Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics.

Jana K. Shen, Yandong Huang, Wei Chen, 2016, The journal of physical chemistry letters.

Electrobiofabrication: electrically based fabrication with biologically derived materials

Jana K. Shen, W. Bentley, Eunkyoung Kim, 2019, Biofabrication.

pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape.

Jana K. Shen, G. Payne, B. Morrow, 2015, Journal of the American Chemical Society.

Assessment of Proton-Coupled Conformational Dynamics of SARS and MERS Coronavirus Papain-like Proteases: Implication for Designing Broad-Spectrum Antiviral Inhibitors

Jana K. Shen, Jack A. Henderson, N. Verma, 2020, bioRxiv.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump.

Jana K. Shen, H. Zgurskaya, Wei Chen, 2017, Journal of chemical theory and computation.

Base-Assisted Mechanism of Acrylamide Reactions With Cysteines: QM/MM Simulations of Afatinib Reaction with EGFR

Jana K. Shen, Shuhua Ma, Heeral Patel, 2024, bioRxiv.

Mechanism and Kinetics of Fentanyl Dissociation from the μ-Opioid Receptor

Christopher R. Ellis, Jana K. Shen, Q. Vo, 2021 .

How μ-opioid receptor recognizes fentanyl

Christopher R. Ellis, Jana K. Shen, Q. Vo, 2021, Nature Communications.

pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL.

Jana K. Shen, Z. Yue, 2018, Physical chemistry chemical physics : PCCP.