Ras Conformational Ensembles, Allostery, and Signaling

The phosphoinositide 3-kinase pathway

Cantley, L. C. (2002) · Science · doi:10.1126/science.296.5573.1655 · Cited by 5,621

ras GENES

Barbacid, M. (1987) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.56.070187.004023 · Cited by 3,885

The GTPase superfamily: conserved structure and molecular mechanism

Bourne, H. R., Sanders, D. A., & McCormick, F. (1991) · Nature · doi:10.1038/349117a0 · Cited by 3,392

Targeting RAS signalling pathways in cancer therapy

Downward, J. (2003) · Nature reviews. Cancer · doi:10.1038/nrc969 · Cited by 3,354

The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism

Engelman, J. A., Luo, J., & Cantley, L. C. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1879 · Cited by 3,330

The Energy Landscapes and Motions of Proteins

Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991) · Science · doi:10.1126/science.1749933 · Cited by 3,250

Targeting the phosphoinositide 3-kinase pathway in cancer

Liu, P., Cheng, H.-L. M., Roberts, T. M., & Zhao, J. J. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd2926 · Cited by 2,785

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A., & Shokat, K. M. (2013) · Nature · doi:10.1038/nature12796 · Cited by 2,557

Small GTP-Binding Proteins

Takai, Y., Sasaki, T., & Matozaki, T. (2001) · Physiological Reviews · doi:10.1152/physrev.2001.81.1.153 · Cited by 2,511

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

Forbes, S. A., Bindal, N., Bamford, S., Cole, C., Kok, C. Y., Beare, D., Jia, M., Shepherd, R., Leung, K., Menzies, A., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq929 · Cited by 2,278

Two Distinct Structures of Membrane‐Associated Homodimers of GTP‐ and GDP‐Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement

Lee, K., Fang, Z., Enomoto, M., Gasmi-Seabrook, G. M. C., Zheng, L., Koide, S., Ikura, M., & Marshall, C. B. (2020) · Angewandte Chemie · doi:10.1002/ange.202001758 · Cited by 15

Microsecond molecular dynamics simulations provide insight into the ATP‐competitive inhibitor‐induced allosteric protection of Akt kinase phosphorylation

Mou, L., Cui, T., Liu, W., Zhang, H., Cai, Z., Lu, S., & Gao, G. (2016) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12895 · Cited by 15

Discovery of Fulzerasib (GFH925) for the Treatment of KRAS G12C-Mutated Solid Tumors

Jiang, T., Lin, C., Le, S., Zhang, L., Liang, T., Cai, L., Lan, X., Ge, M., Liu, Z., He, W., et al. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c03183 · Cited by 14

Reduced dynamic complexity allows structure elucidation of an excited state of KRASG13D

Chao, F.-A., Chan, A. H., Dharmaiah, S., Schwieters, C. D., Tran, T. H., Taylor, T. E., Ramakrishnan, N., Esposito, D., Nissley, D. V., McCormick, F. P., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-04960-6 · Cited by 15

The dynamic nature of the K-Ras/calmodulin complex can be altered by oncogenic mutations

Abdelkarim, H., Leschinsky, N., Jang, H., Banerjee, A., Nussinov, R., & Gaponenko, V. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.06.008 · Cited by 14

The Importance of Mg 2+ ‐Free State in Nucleotide Exchange of Oncogenic K‐Ras Mutants

Pálfy, G., Menyhárd, D. K., Ákontz‐Kiss, H., Vida, I., Batta, G., Tőke, O., & Perczel, A. (2022) · Chemistry - A European Journal · doi:10.1002/chem.202201449 · Cited by 14

KRAS Inhibitor that Simultaneously Inhibits Nucleotide Exchange Activity and Effector Engagement

Pagba, C. V., Gupta, A. K., Naji, A. K., van der Hoeven, D., Churion, K. A., Liang, X., Jakubec, J. L., Höök, M., Zuo, Y., de Kraatz, M. M., et al. (2022) · ACS Bio & Med Chem Au · doi:10.1021/acsbiomedchemau.2c00045 · Cited by 14

Predicting the conformational variability of oncogenic GTP-bound G12D mutated KRas-4B proteins at zwitterionic model cell membranes

Lu, H., & Martı́, J. (2022) · Nanoscale · doi:10.1039/d1nr07622a · Cited by 14

Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect

He, X., Du, K., Wang, Y., Fan, J., Li, M., Ni, D., Lu, S., Bian, X., & Liu, Y. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.860962 · Cited by 13

Allosteric site variants affect GTP hydrolysis on Ras

Johnson, C. W., Fetics, S., Davis, K. P., Rodrigues, J. A., & Mattos, C. (2023) · Protein Science · doi:10.1002/pro.4767 · Cited by 13

Molecular mechanism of regulation of RhoA GTPase by phosphorylation of RhoGDI

Sinha, K., Kumawat, A., Jang, H., Nussinov, R., & Chakrabarty, S. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2023.11.018 · Cited by 13

Activation Mechanism of RhoA Caused by Constitutively Activating Mutations G14V and Q63L

Chen, S., Zhang, Z., Zhang, Y., Choi, T., & Zhao, Y. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232415458 · Cited by 13

Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations

Shi, S., Zheng, L., Ren, Y., & Wang, Z. (2023) · Molecules · doi:10.3390/molecules28072886 · Cited by 13

Robust Strategy for Hit-to-Lead Discovery: NMR for SAR

Larda, S. T., Ayotte, Y., Denk, M. M., Coote, P. W., Heffron, G. J., Bendahan, D., Shahout, F., Girard, N., Iddir, M., Bouchard, P., et al. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.3c00656 · Cited by 13

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 13

Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics

Devanand, T., Venkatraman, P., & Vemparala, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-31234-7 · Cited by 13

In Silico Drug Design of Benzothiadiazine Derivatives Interacting with Phospholipid Cell Membranes

Hu, Z., & Martı́, J. (2022) · Membranes · doi:10.3390/membranes12030331 · Cited by 13

Exploring prognostic genes in ovarian cancer stage-related coexpression network modules

Yang, L., Jing, J., Sun, L., & Yue, Y. (2018) · Medicine · doi:10.1097/md.0000000000011895 · Cited by 13

Proximal Protein Interaction Landscape of RAS Paralogs

Béganton, B., Coyaud, É., Laurent, E. M. N., Mangé, A., Jacquemetton, J., Romancer, M. L., Raught, B., & Solassol, J. (2020) · Cancers · doi:10.3390/cancers12113326 · Cited by 13

Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study

Liang, F., Kang, Z., Sun, X., Chen, J., Duan, X., He, H., & Cheng, J. (2023) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-023-00498-1 · Cited by 12

High pressure 31P NMR spectroscopy on guanine nucleotides

Spoerner, M., Karl, M., Lopes, P., Höring, M., Loeffel, K., Nuehs, A., Adelsberger, J., Kremer, W., & Kalbitzer, H. R. (2016) · Journal of Biomolecular NMR · doi:10.1007/s10858-016-0079-0 · Cited by 12

GLOBAL AND TARGETED PROFILING OF GTP‐BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY

Huang, M., & Wang, Y. (2020) · Mass Spectrometry Reviews · doi:10.1002/mas.21637 · Cited by 12

Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR)

He, X., Ni, D., Zhang, H., Li, X., Zhang, J., Fu, Q., Liu, Y., & Lu, S. (2020) · Scientific Reports · doi:10.1038/s41598-020-70381-8 · Cited by 12

Open Structural Data in Precision Medicine

Nussinov, R., Jang, H., Nir, G., Tsai, C., & Cheng, F. (2022) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-122220-012951 · Cited by 12

The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor

Shi, Y., Cao, S., Ni, D., Fan, J., Lu, S., & Xue, M. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.933676 · Cited by 12

Insight into structural dynamics involved in activation mechanism of full length KRAS wild type and P-loop mutants

Jani, V., Sonavane, U., & Joshi, R. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e36161 · Cited by 12

Theoretical insights into mutation-mediated conformational changes of the GNP-bound H-RAS

Zhao, J., Sun, H., Wang, W., Zhang, L., & Chen, J. (2020) · Chemical Physics Letters · doi:10.1016/j.cplett.2020.138042 · Cited by 11

Molecular dynamics simulations reveal the activation mechanism of mutations G12V and Q61L of Cdc42

Chen, S., Shu, L., Zhao, R., & Zhao, Y. (2022) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26320 · Cited by 11

Bacterial chemoreceptor signaling complexes control kinase activity by stabilizing the catalytic domain of CheA

Tran, T., Mudiyanselage, A. P. K. K. K., Eyles, S. J., & Thompson, L. K. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218467120 · Cited by 11

Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability

Lee, A. A., Kim, N. H., Alvarez, S. A., Ren, H., DeGrandchamp, J. B., Lew, L. J. N., & Groves, J. T. (2024) · Science Advances · doi:10.1126/sciadv.adi0707 · Cited by 11

Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design

Kumar, A. P., Verma, C. S., & Lukman, S. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz161 · Cited by 11

Ligand-mediated conformation diversity of Hsp90 revealed by GaMD simulations and Markov model

Bao, H., Wang, J., Zhao, L., & Chen, J. (2025) · Molecular Diversity · doi:10.1007/s11030-025-11378-1 · Cited by 11

Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation

Özdemir, E. S., Koester, A. M., & Nan, X. (2022) · Genes · doi:10.3390/genes13020219 · Cited by 10

Cluster analysis on conformational changes of the GDP/KRAS complex induced by A59G and D33E

Zhao, J., Wang, L., Bao, H., & Chen, J. (2021) · Chemical Physics Letters · doi:10.1016/j.cplett.2021.138995 · Cited by 10

The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes

Bao, H., Wang, W., Sun, H., & Chen, J. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2213355 · Cited by 10

High-Complexity shRNA Libraries and PI3 Kinase Inhibition in Cancer: High-Fidelity Synthetic Lethality Predictions

Mues, M., Karra, L., Romero–Moya, D., Wandler, A. M., Hangauer, M. J., Ksionda, O., Thus, Y. J., Lindenbergh, M. F., Shannon, K., McManus, M. T., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.045 · Cited by 10

Real-time monitoring of the reaction of KRAS G12C mutant specific covalent inhibitor by in vitro and in-cell NMR spectroscopy

Zhao, Q., Haga, R., Tamura, S., Shimada, I., & Nishida, N. (2023) · Scientific Reports · doi:10.1038/s41598-023-46623-w · Cited by 9

Membrane-Driven Dimerization of the Peripheral Membrane Protein KRAS: Implications for Downstream Signaling

Lee, K. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25052530 · Cited by 9

K-ras peptide mimotope induces a humoral immune response against G12V K-ras antigen in BALB/c mice

Hoo, W. P. Y., Siak, P. Y., Alias, N. A. R., Wong, J. J., Tan, E. W., Song, A. A., Rahim, R. A., & In, L. L. A. (2020) · Asia-Pacific Journal of Molecular Biology and Biotechnology · doi:10.35118/apjmbb.2020.028.3.03 · Cited by 9

Membrane-bound KRAS approximates an entropic ensemble of configurations

Heinrich, F., Van, Q. N., Jean-Francois, F. L., Stephen, A. G., & Lösche, M. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.08.008 · Cited by 9

Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor

Chen, Y., Li, J., Wu, Z., Liu, G., Li, H., Tang, Y., & Li, W. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00914 · Cited by 9

A Structure-Based Allosteric Modulator Design Paradigm

Li, M., Lan, X., Lu, X., & Zhang, J. (2023) · Health Data Science · doi:10.34133/hds.0094 · Cited by 8

Multiscale calculations reveal new insights into the reaction mechanism between KRAS G12C and α, β-unsaturated carbonyl of covalent inhibitors

Yan, X. H., Qu, C., Li, Q., Zhu, L., Tong, H. H. Y., Liu, H., Ouyang, Q., & Yao, X. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.03.027 · Cited by 8

Effector Binding Sequentially Alters KRAS Dimerization on the Membrane: New Insights Into RAS‐Mediated RAF Activation

Lee, S., Eun, H.-J., & Lee, K. (2024) · Advanced Science · doi:10.1002/advs.202401530 · Cited by 8

Designed dualsteric modulators: A novel route for drug discovery

Li, N., Zheng, G., Fu, L., Liu, N., Chen, T., & Lu, S. (2024) · Drug Discovery Today · doi:10.1016/j.drudis.2024.104141 · Cited by 8

Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization

Zhao, D.-R., Yang, J.-T., Liu, M.-T., Yang, L.-Q., & Sang, P. (2025) · RSC Advances · doi:10.1039/d4ra07924h · Cited by 8

Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy

Peacock, D. M., Kelly, M. J. S., & Shokat, K. M. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.2c00566 · Cited by 8

Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics

Haspel, N., Jang, H., & Nussinov, R. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01412 · Cited by 8

Isomer-sourced structure iteration methods for in silico development of inhibitors: Inducing GTP-bound NRAS-Q61 oncogenic mutations to an “off-like” state

Hu, Z., & Martı́, J. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.05.038 · Cited by 8

Differentiating the pre-hydrolysis states of wild-type and A59G mutant HRas: An insight through MD simulations

Sharma, N., Sonavane, U., & Joshi, R. (2017) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2017.05.008 · Cited by 8

The Multi-Level Mechanism of Action of a Pan-Ras Inhibitor Explains its Antiproliferative Activity on Cetuximab-Resistant Cancer Cells

Tisi, R., Spinelli, M., Palmioli, A., Airoldi, C., Cazzaniga, P., Besozzi, D., Nobile, M. S., Mazzoleni, E., Arnhold, S., GIOIA, L. D., et al. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.625979 · Cited by 8

Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas

Sharma, N., Sonavane, U., & Joshi, R. (2020) · PLOS ONE · doi:10.1371/journal.pone.0234836 · Cited by 7

Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set

Tan, Y. S., Chakrabarti, M., Stein, R. M., Prentis, L. E., Rizzo, R. C., Kurtzman, T., Fischer, M. M., & Balius, T. E. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01623 · Cited by 7

How KRAS Mutations Impair Intrinsic GTP Hydrolysis: Experimental and Computational Investigations

Song, L. F., Rabara, D., Bali, S. K., Pei, J., Lau, E. Y., Kirshner, D. A., Lightstone, F. C., McCormick, F., Stephen, A. G., & Yang, Y. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02061 · Cited by 7

Inhibiting synovial inflammation and promoting cartilage repair in rheumatoid arthritis using a matrix metalloproteinase-binding hydrogel

Xue, Z., Li, N., Du, K., Shu, J., Huang, Z., Gao, Z., Xie, X., Li, Q., & Lu, Y. (2025) · Materials Today Bio · doi:10.1016/j.mtbio.2025.101792 · Cited by 7

Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS

Ilter, M., Kaşmer, R., Jalalypour, F., Atılgan, C., Topcu, O., Karakaş, N., & Şensoy, Ö. (2022) · eLife · doi:10.7554/elife.79747 · Cited by 7

Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics

Yu, Z., Wang, Z., Cui, X., Cao, Z., Zhang, W., Sun, K., & Hu, G. (2024) · Molecules · doi:10.3390/molecules29030645 · Cited by 7

Exploring the Lapse in Druggability: Sequence Analysis, Structural Dynamics and Binding Site Characterization of K-RasG12C Variant, a Feasible Oncotherapeutics Target

Adeniji, E. A., Olotu, F. A., & Soliman, M. E. S. (2018) · Anti-Cancer Agents in Medicinal Chemistry · doi:10.2174/1871520618666180718110231 · Cited by 7

Computational Modeling of the Neurofibromin-Stimulated Guanosine Triphosphate Hydrolysis by the KRas Protein

Polyakov, I. V., & Nemukhin, A. V. (2023) · Biophysica · doi:10.3390/biophysica3020025 · Cited by 7

Structure-based prediction of Ras-effector binding affinities and design of “branchegetic” interface mutations

(2023) · doi:10.1016/j.str.2023.04.007 · Cited by 6

Structural Dynamics of Rho GTPases

Lin, Y., & Zheng, Y. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168919 · Cited by 6

Protein structural dynamics in covalent drug design: insights from irreversible and reversible covalent inhibitors

Basu, R., & Fletcher, S. (2026) · RSC Chemical Biology · doi:10.1039/d5cb00230c · Cited by 6

Recent advance of KRAS-G12C inhibitors for cancer therapy

Li, M., Wang, H., Wang, F., Liu, D., Feng, C. L., Yan, G., & Fan, X. (2025) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2025.117878 · Cited by 6

Classification of GTP-dependent K-Ras4B active and inactive conformational states

Narayan, B., Kiel, C., & Buchete, N. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0139181 · Cited by 6

Precise diagnosis and treatment for peripheral T-cell lymphomas: From pathogenic mechanisms to innovative approaches

Qiu, Y., & Zhao, W. (2024) · The Innovation Medicine · doi:10.59717/j.xinn-med.2023.100048 · Cited by 6

Conserved allosteric perturbation of the GTPase domains by region 1 of Ras hypervariable regions

Gu, X. Q., Zhang, Y., & Long, D. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.02.022 · Cited by 6

Dependence of prevalence of contiguous pathways in proteins on structural complexity

Thayer, K. M., Galganov, J. C., & Stein, A. J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0188616 · Cited by 6

Progress in Allosteric Database

Song, K., Zhang, J., & Lu, S. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8719-7_4 · Cited by 6

RAS: Circuitry and therapeutic targeting

Singh, G., Thakur, N., & Kumar, U. (2022) · Cellular Signalling · doi:10.1016/j.cellsig.2022.110505 · Cited by 6

A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by quantum mechanics/molecular mechanics studies

Mooney, M. C., Xu, Y., McClory, J., & Huang, M. (2016) · Theoretical Chemistry Accounts · doi:10.1007/s00214-016-1953-2 · Cited by 6

Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21N-ras and the Resulting GTP Electronic Density

Tichauer, R. H., Favre, G., Cabantous, S., & Brut, M. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b02660 · Cited by 6

Advances in NMR Methods to Identify Allosteric Sites and Allosteric Ligands

Abdelkarim, H., Hitchinson, B., Banerjee, A., & Gaponenko, V. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8719-7_8 · Cited by 6

From oncogenic mutation to dynamic code

Kölch, W., & Kiel, C. (2018) · Science · doi:10.1126/science.aau8059 · Cited by 6

Atomic-level mechanisms of abnormal activation in NRAS oncogenes from two-dimensional free energy landscapes

Hu, Z., & Martı́, J. (2024) · Nanoscale · doi:10.1039/d4nr03372h · Cited by 5

Genetically encodable biosensors for Ras activity

Weeks, R., Mehta, S., & Zhang, J. (2024) · RSC Chemical Biology · doi:10.1039/d3cb00185g · Cited by 5

Dynamic Coupling and Entropy Changes in KRAS G12D Mutation: Insights into Molecular Flexibility, Allostery and Function

Hacisuleyman, A., Yüret, D., & Erman, B. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169075 · Cited by 5

Evolution of structure-guided drug design strategies targeting mutations in codon 12 of KRAS

Dorandish, S., Bhayekar, K., Singh, A., Kushwaha, N. D., Malin, E., Serafimovski, S., Kelm, J. M., Gavande, N. S., & Lakkaniga, N. R. (2025) · RSC Medicinal Chemistry · doi:10.1039/d5md00169b · Cited by 6

Microsecond molecular dynamics simulations and dynamic network analysis provide understanding of the allosteric inactivation of GSK3β induced by the L343R mutation

Li, J., Fu, Q., Liang, Y. Y., Cheng, B., & Li, X. (2019) · Journal of Molecular Modeling · doi:10.1007/s00894-019-4003-x · Cited by 5

Exploration of the selective binding mechanism of GSK3β via molecular modeling and molecular dynamics simulation studies

Mou, L., Ma, Z., Meng, X., Li, W., Liang, S., & Chen, X. (2020) · Medicinal Chemistry Research · doi:10.1007/s00044-020-02514-7 · Cited by 5

Mutagenic Activation of Glutathione Peroxidase-4: Approaches toward Rational Design of Allosteric Drugs

Ma, C., Chung, D. J., Abramson, D. I., Langley, D. R., & Thayer, K. M. (2022) · ACS Omega · doi:10.1021/acsomega.2c01289 · Cited by 5

Interpretable Neural Networks based classifiers for categorical inputsPreprint

Zamuner, S., & Rios, P. D. L. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2102.03202 · Cited by 5

Phosphorylation induces altered protonation states and allosterically regulates Rac1– RhoGDI complex

Sinha, K., Kumawat, A., Jang, H., Nussinov, R., & Chakrabarty, S. (2025) · Protein Science · doi:10.1002/pro.70413 · Cited by 4

Effective drug design screening in bacterial glycolytic enzymes via targeting alternative allosteric sites

Türkmenoğlu, İ., Kurtuluş, G., Sesal, C., Kürkçüoğlu, Ö., Ayyildiz, M., Çeliker, S., Ozhelvaci, F., Du, X., Liu, G. Y., Arditi, M., et al. (2024) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2024.110190 · Cited by 4

Exploring the influence of conserved lysine69 on the catalytic activity of the helicobacter pylori shikimate dehydrogenase: A combined QM/MM and MD simulations

Li, J., Wu, G., Fu, Q., Ge, H., Liu, S., Li, X., & Cheng, B. (2019) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2019.107098 · Cited by 4

143D, a novel selective KRASG12C inhibitor exhibits potent antitumor activity in preclinical models

Xu, L., Zheng, S.-X., Mei, L., Yang, K., Wang, Y., Zhou, Q., Kong, X., Zheng, M.-Y., Jiang, H., & Xie, C. (2023) · Acta Pharmacologica Sinica · doi:10.1038/s41401-023-01053-2 · Cited by 4

Impact of KRAS-G12 Mutations on the KRAS-GTP Bound Conformational Dynamics: Structure, Free Energy Barriers and Drugging Pockets

Hu, Z., Sha, Z., Martı́, J., Guo, S., & Tao, S. (2026) · JACS Au · doi:10.1021/jacsau.5c01097 · Cited by 3

The Gaussian network model as a framework for allosteric analysis: dynamic distance, edge centrality, and entropy sensitivity in KRAS

Erman, B. (2026) · Physical Biology · doi:10.1088/1478-3975/ae3e49 · Cited by 3

Revealing conformational changes of GTP-bound NRAS mutants probed by GaMD and Markov state models

Zhao, L., Wang, J., Ping, H., Yang, W., Cao, H., & Chen, J. (2026) · Physical Chemistry Chemical Physics · doi:10.1039/d5cp04245c · Cited by 3

Real‐Time Visualization of Isoform‐Specific RAF‐KRAS Interactions in Living Cells Using FRET‐BRET Hybrid Biosensors

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Ni, D., Lu, S., & Zhang, J. (2018) · Wiley eBooks · doi:10.1002/9780470027318.a9614 · Cited by 3

Monophthalates of betulinic acid and related pentacyclic triterpenes inhibit efficiently the SOS-mediated nucleotide exchange and impact PI3K/AKT signaling in oncogenic K-RAS4B proteins

Benary, G. E., Kilgenstein, F., Koller, S., & Scherkenbeck, J. (2025) · RSC Advances · doi:10.1039/d4ra08503e · Cited by 2

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