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How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase

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Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery

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KinaMetrix: a web resource to investigate kinase conformations and inhibitor space

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The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning

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Discovery of a hidden transient state in all bromodomain families

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Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors

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Activation Loop Dynamics Are Coupled to Core Motions in Extracellular Signal-Regulated Kinase-2

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Exploring the Ligand Binding/Unbinding Pathway by Selectively Enhanced Sampling of Ligand in a Protein–Ligand Complex

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The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition

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The Conformational Transitions and Dynamics of Burkholderia cepacia Lipase Regulated by Water–Oil Interfaces

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Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors

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Manifold learning in atomistic simulations: a conceptual review

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Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants

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Hidden allosteric sites and De-Novo drug design

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Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization

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Revealing the Unbinding Kinetics and Mechanism of Type I and Type II Protein Kinase Inhibitors by Local-Scaled Molecular Dynamics Simulations

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Caffeoyl-Prolyl-Histidine Amide Inhibits Fyn and Alleviates Atopic Dermatitis-Like Phenotypes via Suppression of NF-κB Activation

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Regulation of protein phosphorylation by PTPN2 and its small-molecule inhibitors/degraders as a potential disease treatment strategy

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TYROSINE KINASES: COMPLEX MOLECULAR SYSTEMS CHALLENGING COMPUTATIONAL METHODOLOGIES

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Identification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach

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Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation

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Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases

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Mechanism of dimer selectivity and binding cooperativity of BRAF inhibitors

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Pressure-Temperature Analysis of the Stability of the CTL9 Domain Reveals Hidden Intermediates

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Finding inhibitors and deciphering inhibitor-induced conformational plasticity in the Janus kinase via multiscale simulations

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All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop.

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Machine learning in nanoscience and beyond: Workflows, data processing, XAI and ITAP metrics, language-based models

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TAB1 binding induced p38α conformation change: an accelerated molecular dynamics simulation study

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Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model

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The multiple-action allosteric inhibition of TYK2 by deucravacitinib: Insights from computational simulations

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Identifying a Feasible Transition Pathway between Two Conformational States for a Protein.

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The novel role of LCK and other PcDEGs in the diagnosis and prognosis of sepsis: Insights from bioinformatic identification and experimental validation

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Dynamic conformational states of apo, ATP and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models

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AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognitionPreprint

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Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey

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Allosteric activation of FGFR2 kinase in endometrial cancer: insights from Gaussian accelerated molecular dynamics and the Markov state model

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Molecular Modeling of Protein Kinases: Current Status and Challenges

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Machine Learning in Molecular Dynamics Simulations of Biomolecular Systems

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‘Piperazining’ the Catalytic Gatekeepers: Unraveling the Pan-Inhibition of SRC Kinases; LYN, FYN and BLK by Masitinib

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Mechanism of dimer selectivity and binding cooperativity of BRAF inhibitorsPreprint

Clayton, J., Romany, A., Matenoglou, E., Gavathiotis, E., Poulikakos, P. I., & Shen, J. (2024) · eLife · doi:10.7554/elife.95334 · Cited by 2 · see citing works

Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transportersPreprint

Weigle, A. T., & Shukla, D. (2024) · bioRxiv · doi:10.1101/2024.06.12.598708 · Cited by 1 · see citing works

Dynamic mechanism for subtype selectivity of endocannabinoids

Dutta, S., Zhao, L., & Shukla, D. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.111434

Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF InhibitorsPreprint

Clayton, J., Romany, A., Matenoglou, E., Gavathiotis, E., Poulikakos, P. I., & Shen, J. (2025) · eLife · doi:10.7554/elife.95334.3 · Cited by 1 · see citing works

Why does Δ 9 -Tetrahydrocannabinol act as a partial agonist of cannabinoid receptors?Preprint

Dutta, S., Selvam, B., Das, A., & Shukla, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.29.441987

The impact of inhibitor size and flexibility on the binding pathways to c-Src kinasePreprint

Shinobu, A., Re, S., & Sugita, Y. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.25.513784

Sequence Controlled Secondary Structure Determines Site-selectivity of LanthipeptidesPreprint

Mi, X., Desormeaux, E. K., Le, T., van der Donk, W. A., & Shukla, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.28.518241

Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF inhibitorsPreprint

Clayton, J., Romany, A., Matenoglou, E., Gavathiotis, E., Poulikakos, P. I., & Shen, J. (2024) · eLife · doi:10.7554/elife.95334.1

Early Aggregation Mechanism of SOD128–38 Based on Force Field Parameter of 5-Cyano-Tryptophan

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Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF InhibitorsPreprint

Clayton, J., Romany, A., Matenoglou, E., Gavathiotis, E., Poulikakos, P. I., & Shen, J. (2024) · eLife · doi:10.7554/elife.95334.2

Intermediate-based virtual screening of c-Kit kinase inhibitors as potential anti-tumor agents via ab inito folding, molecular dynamics simulation, and molecular docking

Jin, L., Qian, C., Wei, Z., Zhang, D., Xi, J., Sun, D., Fu, L., Liu, X., & Zhang, X. (2024) · Arabian Journal of Chemistry · doi:10.1016/j.arabjc.2024.105979

Impact of Inhibitor Size and Flexibility on the Binding Pathways to c-Src Kinase

Shinobu, A., Re, S., Oshima, H., & Sugita, Y. (2026) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.6c02620

BindingDB Entry 50022212: Regulation of protein phosphorylation by PTPN2 and its small-molecule inhibitors/degraders as a potential disease treatment strategy.

BindingDB (2025) · UC San Diego · doi:10.7270/q2d79h3q

BindingDB Entry 50009378: Allosteric Modulator Discovery: From Serendipity to Structure-Based Design.

BindingDB (2021) · UC San Diego · doi:10.7270/q2c53q9m

Lessons from 8 Milliseconds of Aggregated Kinase Molecular Dynamics Simulations

Sultan, M. M., & Pande, V. S. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2017.11.1298

Computational Evaluation of Mutational Effects on Kinase Dynamics

Sultan, M. M., & Pande, V. S. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2015.11.1745

Activation Pathways of Kinases Reveal Intermediate States as Novel Targets for Drug Design

Shukla, D., Roux, B., & Pande, V. S. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2013.11.1784

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

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Studying the Conformational Changes of Protein Kinases Using In Silico Structural Approaches

Shevchenko, E. (2023) · Universitätsbibliothek Tübingen · doi:10.15496/publikation-78023