Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.

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Dynamic personalities of proteins

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From Levinthal to pathways to funnels

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Hyperactive Ras in developmental disorders and cancer

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Catalytic in vivo protein knockdown by small-molecule PROTACs

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The ensemble nature of allostery

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Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association.

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Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders

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Conformational Substates in Proteins

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Structure and dynamics of molecular networks: A novel paradigm of drug discovery

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Is allostery an intrinsic property of all dynamic proteins?

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Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase

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Blocking Oncogenic Ras Signaling for Cancer Therapy

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Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond

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Ras superfamily GEFs and GAPs: validated and tractable targets for cancer therapy?

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Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome

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Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations

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Allostery in Disease and in Drug Discovery

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The RAS/RAF/MEK/ERK and the PI3K/AKT signalling pathways: role in cancer pathogenesis and implications for therapeutic approaches

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Ras history: The saga continues

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Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

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Regulation of RAF protein kinases in ERK signalling

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Allostery and cooperativity revisited

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KRAS: feeding pancreatic cancer proliferation

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Targeting the cancer kinome through polypharmacology

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Folding funnels, binding funnels, and protein function

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The allosteric inhibitor ABL001 enables dual targeting of BCR–ABL1

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Targeting Bcr–Abl by combining allosteric with ATP-binding-site inhibitors

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The Rise of Molecular Glues

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Folding funnels and binding mechanisms

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Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

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Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications

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Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues

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BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas

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Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase

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A dimerization-dependent mechanism drives RAF catalytic activation

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Protein Allostery and Conformational Dynamics

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Transition networks for modeling the kinetics of conformational change in macromolecules.

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Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

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Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

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Drug–target residence time: critical information for lead optimization

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Prolonged and tunable residence time using reversible covalent kinase inhibitors

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Current strategies for the design of PROTAC linkers: a critical review

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Delineating the role of cooperativity in the design of potent PROTACs for BTK

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Binding of 14-3-3 Proteins to the Protein Kinase Raf and Effects on Its Activation

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Targeted protein degraders crowd into the clinic

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A Unified View of “How Allostery Works”

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Anticancer drug resistance: An update and perspective

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Allostery and the Monod-Wyman-Changeux Model After 50 Years

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The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

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Folding and binding cascades: Shifts in energy landscapes

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Driver and Passenger Mutations in Cancer

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Ras Conformational Ensembles, Allostery, and Signaling

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A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS

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Genetic analysis of Ras signalling pathways in cell proliferation, migration and survival

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Allosteric Modulation as a Unifying Mechanism for Receptor Function and Regulation

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Protein folding funnels: the nature of the transition state ensemble

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The next level of complexity: Crosstalk of posttranslational modifications

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Structural and Energetic Basis of Allostery

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Active Ras induces heterodimerization of cRaf and BRaf.

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Allosteric Activation of Functionally Asymmetric RAF Kinase Dimers

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Architecture of autoinhibited and active BRAF–MEK1–14-3-3 complexes

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Small-Molecule Modulation of Protein Homeostasis

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Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

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Drugs for Allosteric Sites on Receptors

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Protein-tyrosine kinases regulate the phosphorylation, protein interactions, subcellular distribution, and activity of p21ras GTPase-activating protein.

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Conformational states dynamically populated by a kinase determine its function

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Opportunities and challenges in the discovery of allosteric modulators of GPCRs for treating CNS disorders

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NMR-based functional profiling of RASopathies and oncogenic RAS mutations

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Protein dynamics and allostery: an NMR view

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Impact of linker length on the activity of PROTACs

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Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

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PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes

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PROTAC-DB: an online database of PROTACs

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Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

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Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation

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Targeting BCR-ABL1 in Chronic Myeloid Leukemia by PROTAC-Mediated Targeted Protein Degradation

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The MEK/ERK Network as a Therapeutic Target in Human Cancer

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Oncogenic and Wild-type Ras Play Divergent Roles in the Regulation of Mitogen-Activated Protein Kinase Signaling

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Allosteric post-translational modification codes

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GTP-Dependent K-Ras Dimerization

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Autoregulation of the Raf-1 serine/threonine kinase

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Strategies for the Selective Regulation of Kinases with Allosteric Modulators: Exploiting Exclusive Structural Features

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Tissue-Specific Oncogenic Activity of KRASA146T

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Allostery and population shift in drug discovery

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Ras proteins in the control of the cell cycle and cell differentiation

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Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view

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PI3K inhibitors: review and new strategies

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Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization

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Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases

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The Underappreciated Role of Allostery in the Cellular Network

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Allosteric enhancers, allosteric agonists and ago-allosteric modulators: where do they bind and how do they act?

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The Best of Both Worlds? Bitopic Orthosteric/Allosteric Ligands of G Protein–Coupled Receptors

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KSR stimulates Raf-1 activity in a kinase-independent manner

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Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling

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Systematic morphological profiling of human gene and allele function via Cell Painting

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Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta

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Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly

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Cancer-derived mutations in the regulatory subunit p85α of phosphoinositide 3-kinase function through the catalytic subunit p110α

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Protein frustratometer: a tool to localize energetic frustration in protein molecules

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A feeling for the numbers in biology

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Kinases and Pseudokinases: Lessons from RAF

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The Different Ways through Which Specificity Works in Orthosteric and Allosteric Drugs

Nussinov, R., & Tsai, C. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212799436377 · Cited by 139 · see citing works

Computational approaches to mapping allosteric pathways

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The interaction of Ras with GTPase‐activating proteins

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Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2

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Landscape and function of multiple mutations within individual oncogenes

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Comment on "The Consensus Coding Sequences of Human Breast and Colorectal Cancers"

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How and when does an anticancer drug leave its binding site?

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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006658 · Cited by 129 · see citing works

Unraveling structural mechanisms of allosteric drug action

Nussinov, R., & Tsai, C.-J. (2014) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2014.03.006 · Cited by 119 · see citing works

Predictability of human differential gene expression

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Allosteric drugs and mutations: chances, challenges, and necessity

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Distinct Binding Preferences between Ras and Raf Family Members and the Impact on Oncogenic Ras Signaling

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The Design of Covalent Allosteric Drugs

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Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures

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Integrated Computational Approaches and Tools for Allosteric Drug Discovery

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Mechanistic and Structural Features of PROTAC Ternary Complexes

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A second molecular biology revolution? The energy landscapes of biomolecular function

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CABS-flex predictions of protein flexibility compared with NMR ensembles

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Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility

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Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin

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Transcription factors and evolution: An integral part of gene expression (Review)

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Affinity Profiling of the Cellular Kinome for the Nucleotide Cofactors ATP, ADP, and GTP

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Functional plasticity and evolutionary adaptation of allosteric regulation

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Folding funnels and conformational transitions via hinge-bending motions

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Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery

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Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex

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Molecular Insights from Conformational Ensembles via Machine Learning

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Structural insights into probe-dependent positive allosterism of the GLP-1 receptor

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Allosteric Modulators: An Emerging Concept in Drug Discovery

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Structure-based prediction of protein allostery

Greener, J. G., & Sternberg, M. J. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.002 · Cited by 91 · see citing works

Structural dynamics is a determinant of the functional significance of missense variants

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Combining Allosteric and Orthosteric Drugs to Overcome Drug Resistance

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AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations

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Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo

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Ras and the Plasma Membrane: A Complicated RelationshipPreprint

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Rational design of allosteric modulators: Challenges and successes

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Transition-state Ensemble in Enzyme Catalysis: Possibility, Reality, or Necessity?

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Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications

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Optimal linker length for small molecule PROTACs that selectively target p38α and p38β for degradation

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The mechanism of activation of monomeric B-Raf V600E

Maloney, R., Zhang, M., Jang, H., & Nussinov, R. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.06.007 · Cited by 83 · see citing works

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

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Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain

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The Strength of Interaction at the Raf Cysteine-Rich Domain Is a Critical Determinant of Response of Raf to Ras Family Small GTPases

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Motions of Allosteric and Orthosteric Ligand-Binding Sites in Proteins are Highly Correlated

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Targeting RAS and PI3K in lung cancer

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Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling

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The Interdependent Activation of Son-of-Sevenless and RasPreprint

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The duality of human oncoproteins: drivers of cancer and congenital disorders

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How multisite phosphorylation impacts the conformations of intrinsically disordered proteins

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Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning

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Structural Mechanisms of PTEN RegulationPreprint

Masson, G. R., & Williams, R. L. (2019) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a036152 · Cited by 75 · see citing works

Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane

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Statistical method on nonrandom clustering with application to somatic mutations in cancer

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Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor

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Emerging Roles for AKT Isoform Preference in Cancer Progression Pathways

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The interplay of structural information and functional studies in kinase drug design: insights from BCR-Abl

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Allosteric Modulation of Human Hsp90α Conformational Dynamics

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A “Tug of War” Maintains a Dynamic Protein–Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane

Li, Z., Prakash, P., & Buck, M. (2018) · ACS Central Science · doi:10.1021/acscentsci.7b00593 · Cited by 71 · see citing works

Inducing protein-protein interactions with molecular glues

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Quantifying Target Occupancy of Small Molecules Within Living Cells

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Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance

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DIRAS3 (ARHI) Blocks RAS/MAPK Signaling by Binding Directly to RAS and Disrupting RAS Clusters

Sutton, M. N., Lü, Z., Li, Y.-C., Zhou, Y., Huang, T., Reger, A. S., Hurwitz, A. M., Palzkill, T. G., Logsdon, C. D., Liang, X., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.045 · Cited by 68 · see citing works

Cushing’s syndrome driver mutation disrupts protein kinase A allosteric network, altering both regulation and substrate specificity

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AlloMAPS: allosteric mutation analysis and polymorphism of signaling database

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Atomic view of the energy landscape in the allosteric regulation of Abl kinase

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The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane

Jang, H., Smith, I. N., Eng, C., & Nussinov, R. (2021) · iScience · doi:10.1016/j.isci.2021.102438 · Cited by 64 · see citing works

Signal transduction pathways involving RAS

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Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

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In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

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Mutational analysis of Raf-1 cysteine rich domain: Requirement for a cluster of basic aminoacids for interaction with phosphatidylserine

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PTEN in Hereditary and Sporadic CancerPreprint

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An allosteric role for receptor activity-modifying proteins in defining GPCR pharmacology

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Mechanical strain promotes skin fibrosis through LRG-1 induction mediated by ELK1 and ERK signalling

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Acute depletion of CTCF rewires genome-wide chromatin accessibility

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The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

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Precision medicine review: rare driver mutations and their biophysical classification

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High-throughput, single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking

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The amino‐terminal B‐Raf‐specific region mediates calcium‐dependent homo‐ and hetero‐dimerization of Raf

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Conformational ensembles, signal transduction and residue hot spots: application to drug discovery.

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How can same-gene mutations promote both cancer and developmental disorders?

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Allosteric Modulators of Sigma-1 Receptor: A Review

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Use of Allosteric Targets in the Discovery of Safer Drugs

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Chemical Switch of a Metabotropic Glutamate Receptor 2 Silent Allosteric Modulator into Dual Metabotropic Glutamate Receptor 2/3 Negative/Positive Allosteric Modulators

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B-Raf autoinhibition in the presence and absence of 14-3-3

Zhang, M., Jang, H., Li, Z., Sacks, D. B., & Nussinov, R. (2021) · Structure · doi:10.1016/j.str.2021.02.005 · Cited by 52 · see citing works

Protein-Tyrosine Kinases Regulate the Phosphorylation, Protein Interactions, Subcellular Distribution, and Activity of p21rasGTPase-Activating Protein

Moran, M. F., Polakis, P. G., McCormick, F. P., Pawson, T. J., & Ellis, C. A. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.4.1804-1812.1991 · Cited by 52 · see citing works

The structural basis for cancer treatment decisions

Nussinov, R., Jang, H., & Tsai, C. (2014) · Oncotarget · doi:10.18632/oncotarget.2439 · Cited by 51 · see citing works

Utilizing protein structure to identify non-random somatic mutations

Ryslik, G. A., Cheng, Y., Cheung, K.-H., Modis, Y., & Zhao, H. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-190 · Cited by 51 · see citing works

On the Allosteric Effect of nsSNPs and the Emerging Importance of Allosteric Polymorphism

Tee, W.-V., Guarnera, E., & Berezovsky, I. N. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.012 · Cited by 51 · see citing works

NMR studies of dynamic biomolecular conformational ensembles

Torchia, D. A. (2014) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2014.11.001 · Cited by 50 · see citing works

Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones

Stetz, G., Tse, A., & Verkhivker, G. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-25329-4 · Cited by 50 · see citing works

Does Ras Activate Raf and PI3K Allosterically?

Nussinov, R., Tsai, C., & Jang, H. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.01231 · Cited by 50 · see citing works

AlphaFold, Artificial Intelligence (AI), and Allostery

Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works

Protein conformational ensembles in function: roles and mechanisms

Nussinov, R., Liu, Y., Zhang, W., & Jang, H. (2023) · RSC Chemical Biology · doi:10.1039/d3cb00114h · Cited by 111 · see citing works

Ligand discovery by activity-based protein profiling

Niphakis, M. J., & Cravatt, B. F. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2024.08.006 · Cited by 90 · see citing works

Molecular glues and induced proximity: An evolution of tools and discovery

Robinson, S. A., Co, J., & Banik, S. M. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2024.04.001 · Cited by 54 · see citing works

Allosteric drugs: New principles and design approaches

Tee, W.-V., & Berezovsky, I. N. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102758 · Cited by 53 · see citing works

Bioinspired Catalyst Design Principles: Progress in Emulating Properties of Enzymes in Synthetic Catalysts

Ginovska, B., Gutiérrez, O. Y., Karkamkar, A., Lee, M., Lercher, J. A., Liu, Y., Raugei, S., Rousseau, R. J., & Shaw, W. J. (2023) · ACS Catalysis · doi:10.1021/acscatal.3c00320 · Cited by 45 · see citing works

Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design

Berezovsky, I. N., & Nussinov, R. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167751 · Cited by 39 · see citing works

CDK2 and CDK4: Cell Cycle Functions Evolve Distinct, Catalysis-Competent Conformations, Offering Drug Targets

Zhang, W., Liu, Y., Jang, H., & Nussinov, R. (2024) · JACS Au · doi:10.1021/jacsau.4c00138 · Cited by 34 · see citing works

Allosteric regulation of autoinhibition and activation of c-Abl

Liu, Y., Zhang, M., Tsai, C., Jang, H., & Nussinov, R. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.08.014 · Cited by 33 · see citing works

Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function

Nussinov, R. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169044 · Cited by 33 · see citing works

DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations

Song, Q., Li, M., Li, Q., Lu, X., Song, K., Zhang, Z., Wei, J., Zhang, L. N., Wei, J., Ye, Y., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad295 · Cited by 28 · see citing works

AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design

Tan, Z. W., Tee, W.-V., Guarnera, E., & Berezovsky, I. N. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac828 · Cited by 28 · see citing works

The value of protein allostery in rational anticancer drug design: an update

Nussinov, R., & Jang, H. (2024) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2024.2384467 · Cited by 29 · see citing works

Allostery Frustrates the Experimentalist

Gianni, S., & Jemth, P. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167934 · Cited by 25 · see citing works

Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design

Colombo, G. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102702 · Cited by 24 · see citing works

Higher‐order interactions of Bcr‐Abl can broaden chronic myeloid leukemia (CML) drug repertoire

Liu, Y., Zhang, M., Jang, H., & Nussinov, R. (2022) · Protein Science · doi:10.1002/pro.4504 · Cited by 20 · see citing works

Allostery in Disease: Anticancer Drugs, Pockets, and the Tumor Heterogeneity Challenge

Nussinov, R., Yavuz, B. R., & Jang, H. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169050 · Cited by 19 · see citing works

Allostery

Montserrat‐Canals, M., Cordara, G., & Krengel, U. (2025) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583524000209 · Cited by 18 · see citing works

Allosteric solution to the problems of undruggable targets, drug toxicity, and emerging resistance

Tee, W.-V., & Berezovsky, I. N. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103172 · Cited by 16 · see citing works

Sequence-dependent model of allosteric communication

Guarnera, E., & Berezovsky, I. N. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0139848 · Cited by 17 · see citing works

Designing drugs and chemical probes with the dualsteric approach

Zha, J., He, J., Wu, C., Zhang, M., Liu, X., & Zhang, J. (2023) · Chemical Society Reviews · doi:10.1039/d3cs00650f · Cited by 14 · see citing works

Binding Modalities and Phase-Specific Regulation of Cyclin/Cyclin-Dependent Kinase Complexes in the Cell Cycle

Bergman, M. T., Zhang, W., Liu, Y., Jang, H., & Nussinov, R. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c03243 · Cited by 13 · see citing works

Pathogenic mutation impairs functional dynamics of Hsp60 in mono- and oligomeric states

Torielli, L., Guarra, F., Shao, H., Gestwicki, J. E., Serapian, S. A., & Colombo, G. (2025) · Nature Communications · doi:10.1038/s41467-025-57958-5 · Cited by 13 · see citing works

ASM variants in the spotlight: A structure-based atlas for unraveling pathogenic mechanisms in lysosomal acid sphingomyelinase

Scrima, S., Lambrughi, M., Tiberti, M., Fadda, E., & Papaleo, E. (2024) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2024.167260 · Cited by 12 · see citing works

Allostery in Disease: From Mutations, Mechanisms, and Signalling Partners to Diagnostic and Drug Therapies

Berezovsky, I. N., & Nussinov, R. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169407 · Cited by 12 · see citing works

Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis

Liu, X., Yang, B., Huang, X., Yan, W., Zhang, Y., & Hu, G. (2023) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-023-00568-w · Cited by 11 · see citing works

ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events

Regev, C., Jang, H., & Nussinov, R. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169130 · Cited by 11 · see citing works

Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR

Deng, J., Yuan, Y., & Cui, Q. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.3c12494 · Cited by 10 · see citing works

Emerging approaches for antagonizing the aryl hydrocarbon receptor

Dvořák, Z., Mani, S., & Vondráček, J. (2025) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2025.05.003 · Cited by 11 · see citing works

Allostery Illuminated: Harnessing AI and Machine Learning for Drug Discovery

Blanco, M.-J., Buskes, M. J., Govindaraj, R. G., Ipsaro, J. J., Prescott-Roy, J., & Padyana, A. K. (2024) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.4c00260 · Cited by 9 · see citing works

Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses

Cui, Q. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.168998 · Cited by 9 · see citing works

Sequence and Structure at Play in Designing Allosteric Drugs and Alleviating the Drug Resistance

Tee, W.-V., Raechell, R., Guarnera, E., & Berezovsky, I. N. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169206 · Cited by 9 · see citing works

How residence time works in allosteric drugs

Nussinov, R., & Jang, H. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103149 · Cited by 10 · see citing works

Synthetic Biology for Designing Allostery and Its Potential Biomedical Applications

Plaper, T., Štibler, U., & Jerala, R. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169225 · Cited by 7 · see citing works

Myristoyl’s dual role in allosterically regulating and localizing Abl kinase

de Buhr, S., & Gräter, F. (2023) · eLife · doi:10.7554/elife.85216 · Cited by 7 · see citing works

Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation

İnan, T., Flinko, R., Lewis, G. K., MacKerell, A. D., & Kürkçüoğlu, Ö. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c00925 · Cited by 7 · see citing works

Network Analysis of Molecular Dynamics Sectors in the p53 Protein

Fabry, J. D., & Thayer, K. M. (2022) · ACS Omega · doi:10.1021/acsomega.2c05635 · Cited by 6 · see citing works

Exploiting allosteric modulation: a new frontier for precision medicine

Alum, E. U., Udechukwu, C. D., & Obasi, D. C. (2025) · Molecular Biology Reports · doi:10.1007/s11033-025-10650-9 · Cited by 5 · see citing works

Coarse grained modelling highlights the binding differences in the two different allosteric sites of the Human Kinesin EG5 and its implications in inhibitor design

Alexandar, S. P., Yennamalli, R. M., & Ulaganathan, V. (2022) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2022.107708 · Cited by 4 · see citing works

Resistance to Allosteric Inhibitors

Outhwaite, I. R., Kwan, I., Leyte-Vidal, A., Shah, N. P., Bahar, İ., & Seeliger, M. A. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169133 · Cited by 4 · see citing works

Tumors and their microenvironments: Learning from pediatric brain pathologies

Nussinov, R., Yavuz, B. R., & Jang, H. (2025) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2025.189328 · Cited by 6 · see citing works

Variable Regions of p53 Isoforms Allosterically Hard Code DNA Interaction

Armour-Garb, I., Han, I. S. M., Cowan, B. S., & Thayer, K. M. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c06229 · Cited by 4 · see citing works

Progressive computational approaches to facilitate decryption of allosteric mechanism and drug discovery

Lu, X., Lan, X., Lu, S., & Zhang, J. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102701 · Cited by 5 · see citing works

Investigation of the mechanism of USP28-mediated IFITM3 elevation in BCR-ABL-dependent imatinib resistance in CML

Li, Z., Xi, Y., Tu, L., Zhang, X., Huang, Y., Nie, H., Peng, C., Chai, H., Zeng, S., Zheng, X., et al. (2024) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2024.116315 · Cited by 3 · see citing works

Deciphering Allosteric Disease Mutations Through Intrinsic Dynamics

Kaskaloglu, B., Duman, O., Kutlu, Y., & Haliloǧlu, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169326 · Cited by 3 · see citing works

Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions

Özdemir, E. S., & Nussinov, R. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1061595 · Cited by 3 · see citing works

Biophysical Insights into Drug Discovery: Leveraging Phase Transitions and Protein Behavior for Therapeutic Innovation

Uzorka, A., Kibirige, D., & Makumbi, D. (2023) · Biophysical Reviews and Letters · doi:10.1142/s1793048023310021 · Cited by 3 · see citing works

Protein Allostery Study in Cells Using NMR Spectroscopy

Chen, X., Zhang, X., Qin, M., Chen, J., Wang, M., Liu, Z., An, L., Song, X., & Yao, L. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c00360 · Cited by 3 · see citing works

Allosteric inhibitors for the treatment of cancers (2021-): A review from medicinal chemistry perspectives

Ma, F., Chen, Y., Ni, Y., He, H., Ji, O., Quan, X., & Qi, B. (2025) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2025.142985 · Cited by 2 · see citing works

Allosteric Cooperativity Mechanism Investigation of Orthosteric and Allosteric Ligands in Modulating AR Activity: A Molecular Dynamics Study

Kong, X., Zou, Y., Cao, P., Dong, Y., Li, K.-C., Zhang, X., Liu, Y., Wu, S., Tian, S., Li, C., et al. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01571 · Cited by 2 · see citing works

Dynamic claw of dengue protease unveils druggability potential with high affinity allosteric inhibitors

Bhunia, M., Misra, R., Maity, A., Mohid, S. A., Kundu, S., Bhunia, A., Maiti, N. C., & Pal, U. (2025) · PNAS Nexus · doi:10.1093/pnasnexus/pgaf276 · Cited by 2 · see citing works

Cyclin-E/A/CDK1/2 Kinetic Landscapes Drive Cell Cycle Phase-Specific Progression and Guide Cyclin-E Degradation Strategy

Zhang, W., Bradburn, D. A., Liu, Y., Jang, H., Kõivomägi, M., & Nussinov, R. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c00279 · Cited by 2 · see citing works

The Allosteric Revolution: From Static Structures to Conformational Ensembles and Next-Generation Therapeutics

Nussinov, R., & Jang, H. (2026) · Journal of Molecular Biology · doi:10.1016/j.jmb.2026.169985 · Cited by 3 · see citing works

A Drug Delivery System for Anticancer Chemotherapy That Targets Efficiency and Reduces the Side Effects of the Gemcitabine Hydrochloride Medicine Using Nanonatural Molecules

El‐Shafai, N. M., Beltagi, A. M., Zanata, S. M., Alotaibi, B. S., Shukry, M., & El‐Mehasseb, I. M. (2025) · ChemistrySelect · doi:10.1002/slct.202501587 · Cited by 2 · see citing works

Computationally Efficient Network Models Successfully Predict Allosteric Sites of SARS ‐ CoV ‐2 Main Protease and Reveal Its Dynamic Allostery

Yuce, M., & Kürkçüoğlu, Ö. (2026) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70122 · Cited by 1 · see citing works

Extending the classical sequence–structure–function paradigm through protein dynamics and context‐dependent behavior

Tripathi, T., Uversky, V. N., & Giuliani, A. (2026) · FEBS Letters · doi:10.1002/1873-3468.70404 · Cited by 1 · see citing works

Decoding the allosteric grammar of protein kinases: A dual‐stream framework integrating protein language models and energy landscape frustration analysis

Gatlin, W., Ludwick, M., Turano, L., Foley, B., Riedlová, K., Škrhák, V., Novotný, M., Hoksza, D., & Verkhivker, G. M. (2026) · Protein Science · doi:10.1002/pro.70714 · Cited by 1 · see citing works

Application of DELs for E3 Ligase Ligand Discovery and Targeted Protein Degradation

Malone, M. L., Sanchez, N. A., Hu, S. L., & Phelps, C. B. (2025) · Royal Society of Chemistry eBooks · doi:10.1039/9781788016032-00134

MultiAlloDriver: a multi-model method to predict and identify cancer driver mutationsPreprint

Zhou, W., Song, Y., He, J., Li, M., Zhang, J., & Lu, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.25.661496

Investigating allostery with atomistic biomolecular simulations

Magni, A., Bonollo, G., Guarra, F., Torielli, L., Moroni, E., Serapian, S. A., & Colombo, G. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-99507-8.00006-8

Understanding the Kinetic Mechanism of Ligands Stabilizing the RAS–CYPA Interaction

Xu, K., Shen, M., Wang, Z., Xiang, S., Deng, Q., Yang, K., Jiang, Z., Wang, Z., Yin, C., Hou, T., et al. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02966

Decoding Allosteric Grammar with Explainable AI Integrating Protein Language Models and Energy Landscape Analysis: Neutral Frustration at Allosteric Binding Sites Encodes Regulatory Versatility in Protein KinasesPreprint

Gatlin, W., Ludwick, M., Turano, L., Foley, B., Riedlová, K., Škrhák, V., Novotný, M., Hoksza, D., & Verkhivker, G. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.21.713412

Beyond ATP: asciminib and the allosteric path in CML

Abruzzese, E. (2026) · Blood · doi:10.1182/blood.2025032327

Entropy-Driven Protein Allosteric Effect in Cells Highlights the Role of Solvation Water Molecules

Zhang, X., Chen, X., Wang, M., Song, X., Wang, Y., & Yao, L. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6c01283

Origins of allostery in vertebrate hemoglobin evolutionPreprint

Cortez-Romero, C. R., Bautista, N. M., Nisler, C. R., Muñiz-Trejo, R., Storz, J. F., & Thornton, J. W. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.25.727495

The cGAS-STING pathway: mechanistic basis, dual biological functions and translational therapeutic advances

Shan, M., Liao, Y., Lin, Z., Song, L., Zhang, W., Jiang, R., Zhang, H., Guo, Y., & Su, F. (2026) · APOPTOSIS · doi:10.1007/s10495-026-02450-8

Targeting the allosteric mechanism of methicillin-resistant Staphylococcus aureus pyruvate kinase: From inhibitor discovery to network reorganization

Yuce, M., Türkmenoğlu, İ., Kurtuluş, G., Sesal, N. C., Akten, E. D., & Kürkçüoğlu, Ö. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.154704

Signal transduction pathways involving RAS

Wiesmüller, L., & Wittinghofer, F. (1994) · Cellular Signalling · doi:10.1016/0898-6568(94)90030-2 · Cited by 63 · see citing works

The value of protein allostery in rational anticancer drug design: an update

Nussinov, R., & Jang, H. (2024) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2024.2384467 · Cited by 29 · see citing works

Abstract 3426: Catalytic degraders effectively address kinase site mutations in EML-ALK oncogenic fusions

Gao, Y., Jiang, B., Kim, H., Che, J., Donovan, K. A., Hatcher, J. M., Huerta, F., Kwiatkowski, N. P., Liu, Y., Liuni, P., et al. (2023) · Cancer Research · doi:10.1158/1538-7445.am2023-3426

Catalytic Degraders Effectively Address Kinase Site Mutations in EML4-ALK Oncogenic Fusions

Gao, Y., Jiang, B., Kim, H., Berberich, M. J., Che, J., Donovan, K. A., Hatcher, J. M., Huerta, F., Kwiatkowski, N. P., Liu, Y., et al. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c01864 · Cited by 50 · see citing works

Imatinib can act as an Allosteric Activator of Abl Kinase

Xie, T., Saleh, T., Rossi, P., Miller, D. J., & Kalodimos, C. G. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167349 · Cited by 23 · see citing works