Controlling Allosteric Networks in Proteins

Collective dynamics of ‘small-world’ networks

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A note on two problems in connexion with graphs

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Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA

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Error and attack tolerance of complex networksPreprint

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Essential dynamics of proteins

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Classes of small-world networks

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Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits *

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Extending the Gaussian network model: integrating local, allosteric, and structural factors for improved residue-residue correlation analysis

Erman, B. (2025) · Physical Biology · doi:10.1088/1478-3975/ae1dc1 · Cited by 1

Computational Analyses of Bifurcated Inter‐Protein Interactions in Protein–Protein Assemblies Reveal Their Pivotal Role in Conferring Stability

Bheemireddy, S., Menon, R., Chavali, S., Sowdhamini, R., & Srinivasan, N. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.70090 · Cited by 1

Heteromerization, Biased Agonism, and Allosteric Modulation of G Protein‐Coupled Receptors in Addiction: Mechanistic Insights and Therapeutic Implications

Alhosaini, K. A., Alanazi, M. M., Alsulaihim, I. N., Alonazi, A. S., Alasmari, F. F., & Khan, M. R. (2026) · Drug Development Research · doi:10.1002/ddr.70273 · Cited by 1

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

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

Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel

Shobair, M., Popov, K., Dang, Y. L., He, H. X., Stutts, M. J., & Dokholyan, N. V. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000604 · Cited by 1

Sparse group selection and analysis of function‐related residue for protein‐state recognition

Bai, F., Puk, K. M., Liu, J., Zhou, H.-Y., Tao, P., Zhou, W., & Wang, S. (2022) · Journal of Computational Chemistry · doi:10.1002/jcc.26937 · Cited by 2

Using Atomistic Simulations to Explore the Role of Methylation and ATP in Chemotaxis Signal Transduction

Joshi, H. N., & Prakash, M. K. (2022) · ACS Omega · doi:10.1021/acsomega.2c00792 · Cited by 1

Dimerization Promotes PKR Activation by Modulating Energetics of αC Helix Conversion between Active and Inactive Conformations

Feinstein, A. G., Cole, J. L., & May, E. R. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c02460 · Cited by 1

An FDA-approved drug structurally and phenotypically corrects the K210del mutation in genetic cardiomyopathy models

Wang, P., Ahmed, M. S., Nguyen, N. U. N., Menendez-Montes, I., Hsu, C., Farag, A., Thet, S., Lam, N. T., Wansapura, J. P., Crossley, E., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci174081 · Cited by 1

Dynamic Structure-Conversion Programming of Metal Complexes in Response to External Stimuli: Chiral Sensing and Achiral Sensing

Miyake, H. (2018) · Bulletin of Japan Society of Coordination Chemistry · doi:10.4019/bjscc.72.38 · Cited by 1

Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins*

Lü, S., Ding, Q., Zhang, M., & Long, M. (2020) · Chinese Physics B · doi:10.1088/1674-1056/abc540 · Cited by 1

Analysis of co-evolved interaction network of E.coli aspartokinase III and regulation of allosteric progress using energy transduction

Wang, S., Ma, C., & Zeng, A. (2021) · Chemical Engineering Journal · doi:10.1016/j.cej.2021.132151 · Cited by 1

Harnessing Shape Complementarity for Upgraded Cyclohexane Purification through Adaptive Bottlenecked Pores in an Imidazole‐Containing MOF

Ye, C., Wang, W., Chen, W., Xiao, Y., Zhang, H., Dai, B., Chen, S., Wu, X., Li, M., & Huang, X. (2021) · Angewandte Chemie · doi:10.1002/ange.202109964 · Cited by 1

Allostery as Structure‐Encoded Collective Dynamics

Shrivastava, I. H., Liu, C., Dutta, A., Bakan, A., & Bahar, İ. (2020) · Wiley eBooks · doi:10.1002/9781118681121.ch6 · Cited by 1

Computational rewiring of allosteric pathways reprograms GPCR selective responses to ligandsPreprint

Kéri, D., Hijazi, M., Oggier, A., & Barth, P. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.30.486353 · Cited by 1

On Numerical Modeling of Equal Channel Angular Extrusion of Ultra High Molecular Weight Polyethylene

Vasylevskyi, K., Miroshnichenko, K., Buklovskyi, S., Tsukrov, I. I., Grover, H., & Citters, D. W. V. (2021) · doi:10.1115/1.0004258v · Cited by 1

A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allosteryPreprint

Liu, Z., Gillis, T., Raman, S., & Cui, Q. (2024) · eLife · doi:10.7554/elife.92262.2 · Cited by 1

characterization of the human monoacylglycerol lipase using mutagenesis, enzyme kinetics and NMR spectroscopy

Rajarshi (2017) · Digital Repository Service (Northeastern University) · doi:10.17760/d20284582

Ligand modulation of allosteric networks in an ancestral steroid receptorPreprint

Okafor, C. D., & Ortlund, E. A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/414375

Deciphering General Characteristics of Residues Constituting Allosteric Communication Paths

Malik, G., Banerji, A., Kouza, M., Buhimschi, I. A., & Kloczkowski, A. (2019) · Lecture notes in computer science · doi:10.1007/978-3-030-17935-9_23

Mapping Co-regulation Pathways among Ligand Binding sites in RyR1Preprint

Chirasani, V. R., Popov, K. I., Meissner, G., & Dokholyan, N. V. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/676841

Developing a Bioscavenger Against Organophosphate Nerve Agents

Jacob, R. B. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/swtm-yd33

Locating and Navigating Energy Transport Networks in Proteins

Reid, K. M., & Leitner, D. M. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-1154-8_4

Unes pàgines "Inèdites" del Dietari d'un pelegrí a Terra Santa

Garolera, N. (1987) · Faig arts

Faculty Opinions recommendation of In silico identification of rescue sites by double force scanning.

Verma, C. S. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.731516352.793552631

A Minimal Approach to the Dynamic Regulation of Biomolecular Conformation

Vossel, M. (2022) · doi:10.53846/goediss-9569

Editor's evaluation: Coevolution-based prediction of key allosteric residues for protein function regulation

Haider, S. M. (2022) · eLife · doi:10.7554/elife.81850.sa0

Neurotoxin Decontamination

Ye, D., & Rempe, S. B. (2023) · IntechOpen eBooks · doi:10.5772/intechopen.110853

Enhancement of SARS-CoV-2 receptor-binding domain activity by two microbial defensins

Gao, B., & Zhu, S. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1195156

Joint Public Review: Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein coupling

(2023) · eLife · doi:10.7554/elife.90773.2.sa1

Allosteric regulation of kinase activity in living cellsPreprint

Godbole, S., & Dokholyan, N. V. (2023) · eLife · doi:10.7554/elife.90574.1

Allosteric regulation of kinase activity in living cellsPreprint

Godbole, S., & Dokholyan, N. V. (2023) · eLife · doi:10.7554/elife.90574.2

Joint Public Review: Allosteric regulation of kinase activity in living cells

(2023) · eLife · doi:10.7554/elife.90574.3.sa0

Author Response: Allosteric regulation of kinase activity in living cells

Godbole, S., & Dokholyan, N. V. (2023) · eLife · doi:10.7554/elife.90574.3.sa2

eLife Assessment: Allosteric regulation of kinase activity in living cells

Dötsch, V. (2023) · eLife · doi:10.7554/elife.90574.3.sa1

Author Response: Allosteric regulation of kinase activity in living cells

Godbole, S., & Dokholyan, N. V. (2023) · eLife · doi:10.7554/elife.90574.4.sa2

Reviewer #2 (Public Review): A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery

(2023) · eLife · doi:10.7554/elife.92262.1.sa1

Reviewer #3 (Public Review): A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery

(2023) · eLife · doi:10.7554/elife.92262.1.sa0

Reviewer #1 (Public Review): A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery

(2023) · eLife · doi:10.7554/elife.92262.1.sa2

Reviewer #1 (Public Review): A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery

(2024) · eLife · doi:10.7554/elife.92262.3.sa1

Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein couplingPreprint

Maria‐Solano, M. A., & Choi, S. (2023) · doi:10.63204/8637.2

Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein couplingPreprint

Maria‐Solano, M. A., & Choi, S. (2023) · doi:10.63204/8637.1

Targeted degradation of Pin1 by an antagonistic peptide enhances gemcitabine therapy in pancreatic cancer

Chen, M., Chu, X., Zhao, H., Ma, L., Meng, J., YanLian, Y. A. N. G., Fang, Q., Fang, X., & Wang, C. (2025) · RSC Medicinal Chemistry · doi:10.1039/d5md00970g

Crystal Packing of Protomers Provides a Valuable Structural Insight into Protein Structure

Lee, D., Ngo, H.-P.-T., Ho, T., Yun, J., Lee, B.-J., Park, Y.-S., Jwa, N., & Kang, L. (2026) · Crystals · doi:10.3390/cryst16040221

Sidechain Dynamics and Allosteric Signaling in a PDZ Domain

Kornev, A. P. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6c01858

Halogen-Bonding-like Interactions Complement Hydrogen Bonding in a Human Flavin-Dependent Dehalogenase

Karmakar, S., & Mishra, S. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c00986

Engineering Protein Circuits for Cellular Control and Precision Immunotherapy

Spina, S. C., Bailey, J., Rajagopal, G., Phan, N., & Kimmel, B. R. (2026) · Chem & Bio Engineering · doi:10.1021/cbe.6c00083

Engineering acid-sensing ion channel 1a with disrupted desensitization: A computer-guided approach

Hassankalhori, M., Hanna, M., Sancho, F., Torras, J., Kellenberger, S. B., & Lucas, M. F. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.154826

BindingDB Entry 50018463: Allosteric inhibitors of the STAT3 signaling pathway.

BindingDB (2024) · UC San Diego · doi:10.7270/q2m90dwx

BindingDB Entry 50013735: A novel class of selective non-nucleoside inhibitors of human DNA methyltransferase 3A.

BindingDB (2022) · UC San Diego · doi:10.7270/q27h1pcj

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

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

Engineering an Allosteric Control of Protein Function

Vishweshwaraiah, Y. L., Chen, J., & Dokholyan, N. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11640 · Cited by 33

Design and engineering of allosteric communications in proteins

Chen, J., Vishweshwaraiah, Y. L., & Dokholyan, N. V. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102334 · Cited by 37

Allosteric Methods and Their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms

Lu, S., Shen, Q., & Zhang, J. (2019) · Accounts of Chemical Research · doi:10.1021/acs.accounts.8b00570 · Cited by 166

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

Allosteric communication and signal transduction in proteins

Wu, N., Barahona, M., & Yaliraki, S. N. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102737 · Cited by 51