Match tier
Listed
Presence
Current · Arkansas
Last published
2026
Sources
OpenAlex · ORCID
Refreshed
2026-08-06
J
Research Areas
Biomedical Subjects
Links
Biography and Research Information
OverviewAI-generated summary
Jana Shen's research focuses on the application of molecular dynamics simulations to investigate complex biological systems, particularly the interactions of proteins and small molecules. Her work utilizes advanced computational techniques, including GPU-accelerated simulations, to explore the thermodynamics, kinetics, and mechanisms underlying these interactions. Shen has published extensively on the development and application of simulation software, such as Amber and CHARMM, contributing to enhancements in their accessibility, functionality, and speed.
A significant area of her research involves studying the recognition and binding mechanisms of opioid receptors with analgesic compounds like fentanyl. This work aims to elucidate how these interactions occur at the molecular level, providing insights into drug efficacy and potential for targeted therapeutic development. Shen also investigates the reactivity of cysteine residues in human kinases, exploring their roles in cellular signaling pathways.
With an h-index of 33 and over 2,900 citations across 133 publications, Shen has established a substantial record of scholarly achievement. She collaborates with other researchers, including Jiahui Chen at the University of Arkansas at Fayetteville, to advance molecular simulation methodologies and their application to pressing biological and medical questions.
Metrics
- h-index: 33
- Publications: 133
- Citations: 2,920
Selected Publications
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Editorial overview: Artificial intelligence methodologies in structural biology: From static snapshots to dynamic and interaction landscapes (2026)
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Slow Dissociation of Nitazenes from the š-Opioid Receptor Underlies the Challenge of Overdose Reversal (2026)
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Slow Dissociation of Nitazenes from the <i>Ī¼</i> -Opioid Receptor Underlies the Challenge of Overdose Reversal (2026)
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How Electric Field Remodels the Nanofibril Structure of Chitosan Hydrogels: The Role of Dewetting during Electro-Assembly (2025)
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Illuminating the Druggable Proteome with an AI Protein Profiling Platform (2025)
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Illuminating the Ligandable Human Proteome with AI Protein Profiling (2025)
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Tribute to Charles L. Brooks III (2025)
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Recent Developments in Amber Biomolecular Simulations (2025)
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Membrane Permeability Drives the Extreme Potency of Fentanyl but not Isotonitazene (2025)
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Drug Resistance Predictions Based on a Directed Flag Transformer (2025)
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How Electric Field Remodels the Nanofibril Structure of Chitosan Hydrogels: the Role of Dewetting During Electro-Assembly (2025)
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Protein Electrostatic Properties are Fine-Tuned Through Evolution (2025)
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Predicting Protein Electrostatics with Protein Language Models (2025)
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A putative binding model of nitazene derivatives at the Ī¼-opioid receptor (2025)
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Author response: Mechanism of dimer selectivity and binding cooperativity of BRAF inhibitors (2025)
Collaboration Network
Top Collaborators
Ruibin Liu
University of Maryland, Baltimore (US)
16 shared publications
- Profiling MAP kinase cysteines for targeted covalent inhibitor design
- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines
- StructureāKinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis
- Quantum Descriptors for Predicting and Understanding the StructureāActivity Relationships of Michael Acceptor Warheads
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Showing 5 of 16 shared publications
Joseph Clayton
University of Maryland, Baltimore (US)
13 shared publications
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
- Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases
- A putative binding model of nitazene derivatives at the Ī¼-opioid receptor
Showing 5 of 13 shared publications
Mingzhe Shen
University of Maryland, Baltimore (US)
9 shared publications
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines
- KaMLs for Predicting Protein p <i>K</i> <sub>a</sub> Values and Ionization States: Are Trees All You Need?
- Interior pH-sensing residue of human voltage-gated proton channel Hv1 is histidine 168
- KaMLs for Predicting Protein p <i>K</i> <sub>a</sub> Values and Ionization States: Are Trees All You Need?
Showing 5 of 9 shared publications
Aarion Romany
9 shared publications
- Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin
- Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases
- Effect of Acetylation on the Nanofibril Formation of Chitosan from All-Atom De Novo Self-Assembly Simulations
- Mechanism of dimer selectivity and binding cooperativity of BRAF inhibitors
- Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin
Showing 5 of 9 shared publications
VinĆcius M. de Oliveira
University of Maryland, Baltimore (US)
8 shared publications
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber
- Constant pH molecular dynamics simulations: Current status and recent applications
- A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Showing 5 of 8 shared publications
Paween Mahinthichaichan
University of Maryland, Baltimore (US)
6 shared publications
- How Ī¼-opioid receptor recognizes fentanyl
- Kinetics and Mechanism of Fentanyl Dissociation from the Ī¼-Opioid Receptor
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
- StructureāKinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis
- An Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
Showing 5 of 6 shared publications
Jack A. Henderson
University of Maryland, Baltimore (US)
6 shared publications
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber
- A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]
- Profiling MAP kinase cysteines for targeted covalent inhibitor design
- Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins
- Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II
Showing 5 of 6 shared publications
Xinyuanyuan Sun
University of LĆ¼beck (DE)
5 shared publications
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
- H172Y mutation perturbs the S1 pocket and nirmatrelvir binding of SARS-CoV-2 main protease through a nonnative hydrogen bond
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K
- An Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
Rolf Hilgenfeld
German Center for Infection Research (DE)
5 shared publications
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
- H172Y mutation perturbs the S1 pocket and nirmatrelvir binding of SARS-CoV-2 main protease through a nonnative hydrogen bond
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
- Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K
- An Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease
Lidiya Stavitskaya
Center for Drug Evaluation and Research (US)
5 shared publications
- StructureāKinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis
- A putative binding model of nitazene derivatives at the Ī¼-opioid receptor
- Machine Learned Classification of Ligand Intrinsic Activities at Human Ī¼-Opioid Receptor
- Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning
- Machine Learned Classification of Ligand Intrinsic Activities at Human <i>Āµ</i> -Opioid Receptor
Gregory F. Payne
Research Institute for Bioscience and Biotechnology (NP)
5 shared publications
- Electro-Biofabrication. Coupling Electrochemical and Biomolecular Methods to Create Functional Bio-Based Hydrogels
- Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin
- Effect of Acetylation on the Nanofibril Formation of Chitosan from All-Atom De Novo Self-Assembly Simulations
- Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin
- How Electric Field Remodels the Nanofibril Structure of Chitosan Hydrogels: The Role of Dewetting during Electro-Assembly
Quynh N. Vo
Center for Drug Evaluation and Research (US)
4 shared publications
- How Ī¼-opioid receptor recognizes fentanyl
- Kinetics and Mechanism of Fentanyl Dissociation from the Ī¼-Opioid Receptor
- StructureāKinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis
- Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning
Christopher R. Ellis
United States Army Combat Capabilities Development Command (US)
4 shared publications
- How Ī¼-opioid receptor recognizes fentanyl
- Kinetics and Mechanism of Fentanyl Dissociation from the Ī¼-Opioid Receptor
- StructureāKinetics Relationships of Opioids from Metadynamics and Machine Learning Analysis
- Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning
Yandong Huang
Jimei University (CN)
4 shared publications
- A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]
- Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins
- Interior pH-sensing residue of human voltage-gated proton channel Hv1 is histidine 168
- Interior pH Sensing Residue of Human Voltage-Gated Proton Channel H <sub>v</sub> 1 is Histidine 168
Ruibin Liu
4 shared publications
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber
- Constant pH molecular dynamics simulations: Current status and recent applications
- Reactivities of the Front Pocket N-Terminal Cap Cysteines in Human Kinases
- Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Covalent Warheads
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