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

Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation

Zhang, H., Ni, D., Fan, J., Li, M.-Y., Zhang, J., Chen, H., Nussinov, R., & Lu, S. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00591 · Cited by 37

A New View of Activating Mutations in Cancer

Nussinov, R., Tsai, C., & Jang, H. (2022) · Cancer Research · doi:10.1158/0008-5472.can-22-2125 · Cited by 36

Specific Substates of Ras To Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments

Li, Y., Zhang, Y., Großerueschkamp, F., Stephan, S., Cui, Q., Kötting, C., Xia, F., & Gerwert, K. B. (2018) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.8b00342 · Cited by 35

Neurodevelopmental disorders, immunity, and cancer are connected

Nussinov, R., Tsai, C., & Jang, H. (2022) · iScience · doi:10.1016/j.isci.2022.104492 · Cited by 35

De-risking Drug Discovery of Intracellular Targeting Peptides: Screening Strategies to Eliminate False-Positive Hits

Ng, S., Juang, Y.-C. A., Chandramohan, A., Kaan, H. Y. K., Sadruddin, A., Yuen, T. Y., Ferrer‐Gago, F. J., Lee, X. C., Liew, X., Johannes, C. W., et al. (2020) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.0c00022 · Cited by 35

Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning

Chen, J., Wang, J., Yang, W., Zhao, L., Zhao, J., & Hu, G. (2024) · Molecules · doi:10.3390/molecules29102317 · Cited by 34

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 34

Molecular Insights into the MAPK Cascade during Viral Infection: Potential Crosstalk between HCQ and HCQ Analogues

Mohanta, T. K., Sharma, N., Arina, P., & Defilippi, P. (2020) · BioMed Research International · doi:10.1155/2020/8827752 · Cited by 34

Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles

Liao, T.-J., Jang, H., Fushman, D., & Nussinov, R. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2018.07.016 · Cited by 34

Computational elucidation of allosteric communication in proteins for allosteric drug design

Ni, D., Liu, Y., Kong, R., Yu, Z., Lu, S., & Zhang, J. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.03.012 · Cited by 33

Prediction of allosteric communication pathways in proteins

Haliloǧlu, T., Hacisuleyman, A., & Erman, B. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac380 · Cited by 33

Plasma membrane phosphatidylinositol 4-phosphate and 4,5-bisphosphate determine the distribution and function of K-Ras4B but not H-Ras proteins

Gulyás, G., Radvánszki, G., Matuska, R., Balla, A., Hunyady, L., Balla, T., & Várnai, P. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.806679 · Cited by 32

Delineating the RAS Conformational Landscape

Parker, M. I., Meyer, J. E., Golemis, E. A., & Dunbrack (2022) · Cancer Research · doi:10.1158/0008-5472.can-22-0804 · Cited by 30

RASSF5: An MST activator and tumor suppressor in vivo but opposite in vitro

Liao, T.-J., Tsai, C., Jang, H., Fushman, D., & Nussinov, R. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.09.001 · Cited by 30

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation

Ni, D., Song, K., Zhang, J., & Lu, S. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18112249 · Cited by 30

Mechanism of activation and the rewired network: New drug design concepts

Nussinov, R., Zhang, M., Maloney, R., Tsai, C., Yavuz, B. R., Tunçbağ, N., & Jang, H. (2021) · Medicinal Research Reviews · doi:10.1002/med.21863 · Cited by 30

Free Energy Profiles Relating With Conformational Transition of the Switch Domains Induced by G12 Mutations in GTP-Bound KRAS

Chen, J., Zhang, S., Zeng, Q., Wang, W., Zhang, Q., & Liu, X. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.912518 · Cited by 30

Conformational Dynamics Allows Sampling of an “Active-like” State by Oncogenic K-Ras-GDP

Grudzien, P. K., Jang, H., Leschinsky, N., Nussinov, R., & Gaponenko, V. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167695 · Cited by 30

Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading

Li, M.-Y., Wang, Y., Fan, J., Zhuang, H., Liu, Y., Ji, D., & Lu, S. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167730 · Cited by 30

PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization

Muratcioğlu, S., Jang, H., Gürsoy, A., Keskin, Ö., & Nussinov, R. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b03035 · Cited by 30

Membrane Thickness as a Key Factor Contributing to the Activation of Osmosensors and Essential Ras Signaling Pathways

Cohen, B. E. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00076 · Cited by 30

Inhibition of Nonfunctional Ras

Nussinov, R., Jang, H., Gürsoy, A., Keskin, Ö., & Gaponenko, V. (2021) · Cell chemical biology · doi:10.1016/j.chembiol.2020.12.012 · Cited by 29

Ras isoform-specific expression, chromatin accessibility, and signaling

Nussinov, R., Zhang, M., Maloney, R., & Jang, H. (2021) · Biophysical Reviews · doi:10.1007/s12551-021-00817-6 · Cited by 29

Current Advances and Trends in KRAS Targeted Therapies for Colorectal Cancer

Teo, M. Y. M., Fong, J. Y., Lim, W. M., & In, L. L. A. (2021) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-21-0248 · Cited by 28

The Influence of Oncogenic RAS on Chemotherapy and Radiotherapy Resistance Through DNA Repair Pathways

Cáceres-Gutiérrez, R. E., Alfaro‐Mora, Y., Andonegui, M. A., Díaz‐Chávez, J., & Herrera, L. A. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.751367 · Cited by 28

Computer-Aided Drug Design Boosts RAS Inhibitor Discovery

Wang, G., Bai, Y., Cui, J., Zong, Z., Gao, Y., & Zheng, Z. (2022) · Molecules · doi:10.3390/molecules27175710 · Cited by 28

Allosteric activation of RAF in the MAPK signaling pathway

Tsai, C., & Nussinov, R. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.07.007 · Cited by 27

Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics

Haspel, N., Jang, H., & Nussinov, R. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.12.007 · Cited by 27

The Ras dimer structure

Rudack, T., Teuber, C., Scherlo, M., Güldenhaupt, J., Schartner, J., Lübben, M., Klare, J. P., Gerwert, K. B., & Kötting, C. (2021) · Chemical Science · doi:10.1039/d1sc00957e · Cited by 27

Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations

Bao, H., Wang, W., Sun, H., & Chen, J. (2023) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2023.2195995 · Cited by 27

Multiple Strategies to Develop Small Molecular KRAS Directly Bound Inhibitors

Zhou, X., Ji, Y., & Zhou, J. (2023) · Molecules · doi:10.3390/molecules28083615 · Cited by 27

Excited-state observation of active K-Ras reveals differential structural dynamics of wild-type versus oncogenic G12D and G12C mutants

Hansen, A. L., Xiang, X., Yuan, C., Bruschweiler‐Li, L., & Brüschweiler, R. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01070-z · Cited by 27

Computational Insights into the Interactions between Calmodulin and the c/nSH2 Domains of p85α Regulatory Subunit of PI3Kα: Implication for PI3Kα Activation by Calmodulin

Ni, D., Liu, D., Zhang, J., & Lu, S. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19010151 · Cited by 26

Trametinib overcomes KRAS‐G12V–induced osimertinib resistance in a leptomeningeal carcinomatosis model of EGFR‐mutant lung cancer

Fukuda, K., Otani, S., Takeuchi, S., Arai, S., Nanjo, S., Tanimoto, A., Nishiyama, A., Naoki, K., & Yano, S. (2021) · Cancer Science · doi:10.1111/cas.15035 · Cited by 26

E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form

Johansen, J., Kavaliauskas, D., Pfeil, S. H., Blaise, M., Cooperman, B. S., Goldman, Y. E., Thirup, S., & Knudsen, C. R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky697 · Cited by 26

Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRAS G12C and ARS compounds

Khrenova, M. G., Kulakova, A. M., & Nemukhin, A. V. (2020) · Organic & Biomolecular Chemistry · doi:10.1039/d0ob00071j · Cited by 26

Dynamically encoded reactivity of Ras enzymes: opening new frontiers for drug discovery

Pálfy, G., Menyhárd, D. K., & Perczel, A. (2020) · Cancer and Metastasis Reviews · doi:10.1007/s10555-020-09917-3 · Cited by 26

Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography

Girard, É., Lopes, P., Spoerner, M., Dhaussy, A., Prangé, T., Kalbitzer, H. R., & Colloc’h, N. (2022) · Chemical Science · doi:10.1039/d1sc05488k · Cited by 25

Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics

Chao, F.-A., Dharmaiah, S., Taylor, T. E., Messing, S. A. J., Gillette, W., Esposito, D., Nissley, D. V., McCormick, F. P., Byrd, R. A., Simanshu, D. K., et al. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c00007 · Cited by 25

Exploring CRD mobility during RAS/RAF engagement at the membrane

Nguyen, K., López, C. A., Neale, C., Van, Q. N., Carpenter, T. S., Natale, F. D., Travers, T. S., Tran, T. H., Chan, A. H., Bhatia, H., et al. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.06.035 · Cited by 25

RAS‐targeted cancer therapy: Advances in drugging specific mutations

Liu, C., Ye, D., Yang, H., Chen, X., Su, Z., Li, X., Ding, M., & Liu, Y. (2023) · MedComm · doi:10.1002/mco2.285 · Cited by 25

The dynamic mechanism of RASSF5 and MST kinase activation by Ras

Liao, T.-J., Jang, H., Tsai, C., Fushman, D., & Nussinov, R. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp08596b · Cited by 25

Common mechanisms of catalysis in small and heterotrimeric GTPases and their respective GAPs

Gerwert, K. B., Mann, D., & Kötting, C. (2017) · Biological Chemistry · doi:10.1515/hsz-2016-0314 · Cited by 25

Oncogenic KRas mobility in the membrane and signaling response

Nussinov, R., Tsai, C., & Jang, H. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.02.009 · Cited by 25

Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis

Zeng, J., Weng, J., Zhang, Y., Xia, F., Cui, Q., & Xu, X. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c04679 · Cited by 24

Fluorescent Biosensor for Measuring Ras Activity in Living Cells

Weeks, R., Zhou, X., Yuan, T. L., & Zhang, J. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c05203 · Cited by 24

Diversity of mechanisms in Ras–GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling

Grigorenko, B. L., Kots, E. D., & Nemukhin, A. V. (2019) · Organic & Biomolecular Chemistry · doi:10.1039/c9ob00463g · Cited by 24

Toward the Design of Allosteric Effectors: Gaining Comprehensive Control of Drug Properties and Actions

Tee, W.-V., Lim, S. J. M., & Berezovsky, I. N. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c01043 · Cited by 23

Molecular dynamics simulations provide insights into the origin of gleevec’s selectivity toward human tyrosine kinases

Wang, L., Zheng, G., Liu, X., Ni, D., He, X., Cheng, J., & Lu, S. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2018.1496139 · Cited by 23

Pan-RAS inhibitors: Hitting multiple RAS isozymes with one stone

Coley, A. B., Ward, A., Keeton, A. B., Chen, X., Maxuitenko, Y. Y., Prakash, A., Li, F., Foote, J. B., Buchsbaum, D. J., & Piazza, G. A. (2022) · Advances in cancer research · doi:10.1016/bs.acr.2021.07.009 · Cited by 23

Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C

Zhuang, H., Fan, J., Li, M., Zhang, H., Yang, X., Lin, L., Lu, S., Wang, Q., & Liu, Y. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.915512 · Cited by 23

Allosteric modulators of MEK1: drug design and discovery

Shang, J., Lu, S., Jiang, Y., & Zhang, J. (2016) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12780 · Cited by 23

Lipid-Mediated Regulation of Embedded Receptor Kinases via Parallel Allosteric Relays

Ghosh, M., Wang, L. C., Ramesh, R., Morgan, L. K., Kenney, L. J., & Anand, G. S. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2016.12.027 · Cited by 23

Single-molecule fluorescence imaging of RalGDS on cell surfaces during signal transduction from Ras to Ral

Yoshizawa, R., Umeki, N., Yanagawa, M., Murata, M., & Sako, Y. (2017) · Biophysics and Physicobiology · doi:10.2142/biophysico.14.0_75 · Cited by 23

Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs?

An, X., Lu, S., Song, K., Shen, Q., Huang, M., Yao, X., Liu, H., & Zhang, J. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00735 · Cited by 23

Molecular dynamics simulations reveal the allosteric effect of F1174C resistance mutation to ceritinib in ALK-associated lung cancer

Ni, Z., Wang, X., Zhang, T., & Jin, R. (2016) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2016.10.005 · Cited by 23

Characteristics of Allosteric Proteins, Sites, and Modulators

He, X., Ni, D., Lu, S., & Zhang, J. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8719-7_6 · Cited by 22

Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics

Eren, M., Tunçbağ, N., Jang, H., Nussinov, R., Gürsoy, A., & Keskin, Ö. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c00891 · Cited by 22

How Parkinson's disease-related mutations disrupt the dimerization of WD40 domain in LRRK2: a comparative molecular dynamics simulation study

Li, X., Ye, M., Wang, Y., Qiu, M., Fu, T., Zhang, J., Zhou, B., & Lu, S. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp03171b · Cited by 22

Unveiling the “invisible” druggable conformations of GDP-bound inactive Ras

Liu, D., Mao, Y., Gu, X., Zhou, Y., & Long, D. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024725118 · Cited by 22

Deciphering the Mechanism of Gilteritinib Overcoming Lorlatinib Resistance to the Double Mutant I1171N/F1174I in Anaplastic Lymphoma Kinase

Liang, S., Wang, Q., Qi, X., Liu, Y., Li, G., Lu, S., Mou, L., & Chen, X. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.808864 · Cited by 21

Regulation of GTPase function by autophosphorylation

Johnson, C. W., Seo, H., Terrell, E. M., Yang, M.-H., KleinJan, F., Gebregiworgis, T., Gasmi-Seabrook, G. M. C., Geffken, E. A., Lakhani, J., Song, K., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.02.011 · Cited by 21

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

Halakou, F., Sen-Kilic, E., Cukuroglu, E., Keskin, Ö., & Gürsoy, A. (2017) · Scientific Reports · doi:10.1038/s41598-017-07351-0 · Cited by 21

Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations

Yan, F., Liu, X., Zhang, S., Su, J., Zhang, Q., & Chen, J. (2017) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2017.1394221 · Cited by 21

Calmodulin and IQGAP1 activation of PI3Kα and Akt in KRAS, HRAS and NRAS-driven cancers

Nussinov, R., Zhang, M., Tsai, C., & Jang, H. (2017) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2017.10.032 · Cited by 21

Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations

Chen, J., Wang, J., Lai, F., Wang, W., Pang, L., & Zhu, W. (2018) · RSC Advances · doi:10.1039/c8ra05042b · Cited by 21

Extending the Lifetime of Native GTP‐Bound Ras for Site‐Resolved NMR Measurements: Quantifying the Allosteric Dynamics

Chen, X., Yao, H., Wang, H., Mao, Y., Liu, D., & Long, D. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201812902 · Cited by 21

Long-lasting Salt Bridges Provide the Anchoring Mechanism of Oncogenic Kirsten Rat Sarcoma Proteins at Cell Membranes

Lu, H., & Martı́, J. (2020) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.0c02809 · Cited by 21

Independent and core pathways in oncogenic KRAS signaling

Nussinov, R., Tsai, C., & Jang, H. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2016.1209417 · Cited by 21

Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process

Xiong, Y., Zeng, J., Xia, F., Cui, Q., Deng, X., & Xu, X. (2022) · Journal of Computational Chemistry · doi:10.1002/jcc.26846 · Cited by 20

Engineering subtilisin proteases that specifically degrade active RAS

Chen, Y., Toth, E. A., Ruan, B., Choi, E. J., Simmerman, R. F., Chen, Y., He, Y., Wang, R., Godoy‐Ruiz, R., King, H., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01818-7 · Cited by 20

SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations

Liao, T.-J., Jang, H., Fushman, D., & Nussinov, R. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0013926 · Cited by 20

Allostery

Montserrat‐Canals, M., Cordara, G., & Krengel, U. (2025) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583524000209 · Cited by 19

Targeted Degradation Technologies Utilizing Autophagy

Zhou, Z., Liang, J., Cheng, B., Li, Y., Zhou, W., Tian, H., Shi, W., Liu, K., Fang, L., Li, H., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26146576 · Cited by 19

Theoretical insight into molecular mechanisms of inhibitor bindings to bromodomain-containing protein 4 using molecular dynamics simulations and calculations of binding free energies

Wang, L., Wang, Y., Sun, H., Zhao, J., & Wang, Q. (2019) · Chemical Physics Letters · doi:10.1016/j.cplett.2019.136785 · Cited by 19

A comprehensive toxicity evaluation in rats after long-term oral Gelsemium elegans exposure

Zuo, M., Wu, Y., Wang, Z., Wang, N., Huang, S.-J., Yu, H., Zhao, X., Huang, C.-Y., & Liu, Z. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.111284 · Cited by 19

Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling

Muratcioğlu, S., Aydın, C., Odabasi, E., Özdemir, E. S., Firat‐Karalar, E. N., Jang, H., Tsai, C., Nussinov, R., Kavaklı, İ. H., Gürsoy, A., et al. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.01.002 · Cited by 19

Sensitive, enzyme-free and label-free electrochemical sensor for K-ras G12D point mutation detection based on double cascade amplification reaction

Zhou, X., Liu, X., Xia, X., Yang, X., & Xiang, H. (2020) · Journal of Electroanalytical Chemistry · doi:10.1016/j.jelechem.2020.114270 · Cited by 19

Dynamic Protein Allosteric Regulation and Disease

Nussinov, R., Tsai, C.-J., & Jang, H. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-981-13-8719-7_2 · Cited by 18

Drug resistance and tumor heterogeneity: cells and ensembles

Nussinov, R., Yavuz, B. R., & Jang, H. (2025) · Biophysical Reviews · doi:10.1007/s12551-025-01320-y · Cited by 18

Ras superfamily GTPase activating proteins in cancer: Potential therapeutic targets?

Xiao, H., Wang, G., Zhao, M., Wen, S., Ouyang, L., & Sun, Q. (2023) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2023.115104 · Cited by 18

Binding modes of GDP, GTP and GNP to NRAS deciphered by using Gaussian accelerated molecular dynamics simulations

Bao, H., Wang, W., Sun, H. B., & Chen, J. Z. (2023) · SAR and QSAR in environmental research · doi:10.1080/1062936x.2023.2165542 · Cited by 18

Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques

Zha, J., Li, M., Kong, R., Lu, S., & Zhang, J. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167481 · Cited by 18

Developments in integrative modeling with dynamical interfaces

Ozdemir, E. S., Nussinov, R., Gursoy, A., & Keskin, O. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.10.007 · Cited by 17

Allosteric Nucleic Acid Enzyme: A Versatile Stimuli‐Responsive Tool for Molecular Computing and Biosensing Nanodevices

Hu, Y., Li, C., Hu, M., Zhang, Z., Fu, R., Tang, X., & Wu, T. (2023) · Small · doi:10.1002/smll.202300207 · Cited by 17

Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production

Wu, M., Sun, Y., Zhu, M., Zhu, L., Lü, J., & Geng, F. (2021) · ACS Omega · doi:10.1021/acsomega.1c00798 · Cited by 17

The Self‐Association of the KRAS4b Protein is Altered by Lipid‐Bilayer Composition and Electrostatics

Lee, K., Ikura, M., & Marshall, C. B. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202218698 · Cited by 17

The protonation states of GTP and GppNHp in Ras proteins

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