Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.

Monod, J., Wyman, J., & Changeux, J. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80285-6 · Cited by 7,681

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

Protacs: Chimeric molecules that target proteins to the Skp1–Cullin–F box complex for ubiquitination and degradation

Sakamoto, K. M., Kim, K. B., Kumagai, A., Mercurio, F., Crews, C. M., & Deshaies, R. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.141230798 · Cited by 2,609

Dynamic personalities of proteins

Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545

From Levinthal to pathways to funnels

Dill, K. A., & Chan, H. S. (1997) · Nature Structural & Molecular Biology · doi:10.1038/nsb0197-10 · Cited by 2,293

THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

Onuchic, J. N., Luthey-Schulten, Z., & Wolynes, P. G. (1997) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.48.1.545 · Cited by 2,210

RAS oncogenes: weaving a tumorigenic web

Pylayeva-Gupta, Y., Grabocka, E., & Bar-Sagi, D. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3106 · Cited by 1,789

Shared and distinct transcriptomic cell types across neocortical areas

Tasic, B., Yao, Z., Graybuck, L. T., Smith, K. A., Nguyen, T. N., Bertagnolli, D., Goldy, J., Garren, E., Economo, M. N., Viswanathan, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0654-5 · Cited by 1,746

Hyperactive Ras in developmental disorders and cancer

Schubbert, S., Shannon, K., & Bollag, G. (2007) · Nature Reviews Cancer · doi:10.1038/nrc2109 · Cited by 1,583

Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions

Kölch, W. (2000) · Biochemical Journal · doi:10.1042/bj3510289 · Cited by 1,443

Catalytic in vivo protein knockdown by small-molecule PROTACs

Bondeson, D. P., Mares, A., Smith, I. E. D., Ko, E., Campos, S., Miah, A. H., Mulholland, K. E., Routly, N., Buckley, D. L., Gustafson, J. L., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1858 · Cited by 1,356

The ensemble nature of allostery

Motlagh, H. N., Wrabl, J. O., Li, J., & Hilser, V. J. (2014) · Nature · doi:10.1038/nature13001 · Cited by 1,247

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

Jeffrey Conn, P., Christopoulos, A., & Lindsley, C. W. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd2760 · Cited by 1,063

Crystal Structure of the PTEN Tumor Suppressor

Lee, J., Yang, H., Georgescu, M.-M., Cristofano, A. D., Maehama, T., Shi, Y., Dixon, J. E., Pandolfi, P. P., & Pavletich, N. P. (1999) · Cell · doi:10.1016/s0092-8674(00)81663-3 · Cited by 1,032

Conformational Substates in Proteins

Frauenfelder, H., Parak, F., & Young, R. D. (1988) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.17.060188.002315 · Cited by 995

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

Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 905

Is allostery an intrinsic property of all dynamic proteins?

Gunasekaran, K., Ma, B., & Nussinov, R. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20232 · Cited by 896

Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase

Nagar, B., Hantschel, O. D., Young, M. A., Scheffzek, K., Veach, D. R., Bornmann, W. G., Clarkson, B., Superti‐Furga, G., & Kuriyan, J. (2003) · Cell · doi:10.1016/s0092-8674(03)00194-6 · Cited by 880

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

Holderfield, M. T., Deuker, M. M., McCormick, F. P., & McMahon, M. (2014) · Nature reviews. Cancer · doi:10.1038/nrc3760 · Cited by 850

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

Vigil, D., Cherfils, J., Rossman, K. L., & Der, C. J. (2010) · Nature reviews. Cancer · doi:10.1038/nrc2960 · Cited by 850

Blocking Oncogenic Ras Signaling for Cancer Therapy

Adjei, A. A. (2001) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/93.14.1062 · Cited by 836

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

Davoli, T., Xu, A. W., Mengwasser, K. E., Sack, L. M., Yoon, J. C., Park, P. J., & Elledge, S. J. (2013) · Cell · doi:10.1016/j.cell.2013.10.011 · Cited by 815

Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations

Hunter, J. C., Manandhar, A., Carrasco, M. A., Gurbani, D., Gondi, S., & Westover, K. D. (2015) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-15-0203 · Cited by 786

Allostery in Disease and in Drug Discovery

Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 769

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

Luca, A. D., Maiello, M. R., D’Alessio, A., Pergameno, M., & Normanno, N. (2012) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728222.2011.639361 · Cited by 748

Ras history: The saga continues

Cox, A. D., & Der, C. J. (2010) · Small GTPases · doi:10.4161/sgtp.1.1.12178 · Cited by 706

Regulation of RAF protein kinases in ERK signalling

Lavoie, H., & Therrien, M. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3979 · Cited by 702

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

Keskin, O., Gursoy, A., Ma, B., & Nussinov, R. (2008) · Chemical Reviews · doi:10.1021/cr040409x · Cited by 697

KRAS: feeding pancreatic cancer proliferation

Bryant, K. L., Mancias, J. D., Kimmelman, A. C., & Der, C. J. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2013.12.004 · Cited by 693

Allostery and cooperativity revisited

Cui, Q., & Karplus, M. (2008) · Protein Science · doi:10.1110/ps.03259908 · Cited by 684

Targeting the cancer kinome through polypharmacology

Knight, Z. A., Lin, H., & Shokat, K. M. (2010) · Nature reviews. Cancer · doi:10.1038/nrc2787 · Cited by 674

Folding funnels, binding funnels, and protein function

Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science · doi:10.1110/ps.8.6.1181 · Cited by 648

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

Zhang, J., Adrián, F., Jahnke, W., Cowan‐Jacob, S. W., Li, A. G., Iacob, R. E., Sim, T., Powers, J. T., Dierks, C., Sun, F., et al. (2010) · Nature · doi:10.1038/nature08675 · Cited by 623

The allosteric inhibitor ABL001 enables dual targeting of BCR–ABL1

Wylie, A. A., Schoepfer, J. G., Jahnke, W., Cowan‐Jacob, S. W., Loo, A. T., Furet, P., Marzinzik, A. L., Pellé, X., Donovan, J., Zhu, W. S., et al. (2017) · Nature · doi:10.1038/nature21702 · Cited by 622

The Rise of Molecular Glues

Schreiber, S. L. (2021) · Cell · doi:10.1016/j.cell.2020.12.020 · Cited by 598

Folding funnels and binding mechanisms

Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594

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

Raghavan, S., Winter, P. S., Navia, A. W., Williams, H. L., DenAdel, A., Lowder, K. E., Galvez-Reyes, J., Kalekar, R. L., Mulugeta, N., Kapner, K. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.11.017 · Cited by 592

Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications

Bah, A., & Forman-Kay, J. D. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.r115.695056 · Cited by 557

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

Keskin, O., Ma, B., & Nussinov, R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.077 · Cited by 519

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

Pfister, S. M., Janzarik, W. G., Remke, M., Ernst, A., Werft, W., Becker, N., Toedt, G., Wittmann, A., Kratz, C. P., Olbrich, H., et al. (2008) · Journal of Clinical Investigation · doi:10.1172/jci33656 · Cited by 518

Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase

Smith, B. E., Wang, S. L., Jaime-Figueroa, S., Harbin, A., Wang, J., Hamman, B. D., & Crews, C. M. (2019) · Nature Communications · doi:10.1038/s41467-018-08027-7 · Cited by 517

A dimerization-dependent mechanism drives RAF catalytic activation

Rajakulendran, T., Sahmi, M., Lefrançois, M., Sicheri, F., & Therrien, M. (2009) · Nature · doi:10.1038/nature08314 · Cited by 505

Protein Allostery and Conformational Dynamics

Guo, J., & Zhou, H.-X. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00590 · Cited by 484

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

Noé, F., & Fischer, S. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.01.008 · Cited by 450

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

Carter, H. K., Chen, S., Işık, L., Tyekucheva, S., Velculescu, V. E., Kinzler, K. W., Vogelstein, B., & Karchin, R. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-1133 · Cited by 448

Drug–target residence time: critical information for lead optimization

Lu, H., & Tonge, P. J. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.06.176 · Cited by 440

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

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436

Prolonged and tunable residence time using reversible covalent kinase inhibitors

Bradshaw, J. M., McFarland, J. M., Paavilainen, V. O., Bisconte, A. R., Tam, D., Phan, V. T., Romanov, S., Finkle, D., Shu, J., Patel, V. P., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1817 · Cited by 433

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

Troup, R. I., Fallan, C., & Baud, M. G. J. (2020) · Exploration of Targeted Anti-tumor Therapy · doi:10.37349/etat.2020.00018 · Cited by 424

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

Zorba, A., Nguyen, C., Xu, Y., Starr, J., Borzilleri, K., Smith, J., Zhu, H., Farley, K. A., Ding, W., Schiemer, J., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1803662115 · Cited by 419

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

Freed, E., Symons, M. H., Macdonald, S. G., McCormick, F. P., & Ruggieri, R. (1994) · Science · doi:10.1126/science.8085158 · Cited by 414

Targeted protein degraders crowd into the clinic

Mullard, A. (2021) · Nature Reviews Drug Discovery · doi:10.1038/d41573-021-00052-4 · Cited by 409

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

Changeux, J. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-050511-102222 · Cited by 406

Anticancer drug resistance: An update and perspective

Nussinov, R., Tsai, C., & Jang, H. (2021) · Drug Resistance Updates · doi:10.1016/j.drup.2021.100796 · Cited by 403

A Unified View of “How Allostery Works”

Tsai, C.-J., & Nussinov, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003394 · Cited by 401

Driver and Passenger Mutations in Cancer

Pon, J. R., & Marra, M. A. (2014) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-012414-040312 · Cited by 380

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

del Sol, A., Tsai, C., Ma, B., & Nussinov, R. (2009) · Structure · doi:10.1016/j.str.2009.06.008 · Cited by 367

Folding and binding cascades: Shifts in energy landscapes

Tsai, C.-J., Ma, B., & Nussinov, R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.9970 · Cited by 365

Ras Conformational Ensembles, Allostery, and Signaling

Lu, S., Jang, H., Muratcioglu, S., Gursoy, A., Keskin, O., Nussinov, R., & Zhang, J. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00542 · Cited by 355

Allosteric Modulation as a Unifying Mechanism for Receptor Function and Regulation

Changeux, J., & Christopoulos, A. (2016) · Cell · doi:10.1016/j.cell.2016.08.015 · Cited by 353

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

Huang, W. Y. C., Alvarez, S. A., Kondo, Y., Lee, Y. K., Chung, J. K., Lam, H. Y. M., Biswas, K. H., Kuriyan, J., & Groves, J. T. (2019) · Science · doi:10.1126/science.aau5721 · Cited by 352

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

Drosten, M., Dhawahir, A., Sum, E. Y. M., Urosevic, J., Lechuga, C. G., Esteban, L. M., Castellano, E., Guerra, C., Santos, E., & Barbacid, M. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.7 · Cited by 347

The next level of complexity: Crosstalk of posttranslational modifications

Venne, A. S., Kollipara, L., & Zahedi, R. P. (2013) · PROTEOMICS · doi:10.1002/pmic.201300344 · Cited by 331

Protein folding funnels: the nature of the transition state ensemble

Onuchic, J. N., Socci, N. D., Luthey-Schulten, Z. A., & Wolynes, P. G. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00060-0 · Cited by 330

Identification of the major phosphorylation sites of the Raf-1 kinase

Morrison, D. K., Heidecker, G., Rapp, U. R., & Copeland, T. D. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)85336-x · Cited by 328

Structural and Energetic Basis of Allostery

Hilser, V. J., Wrabl, J. O., & Motlagh, H. N. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-050511-102319 · Cited by 321

Active Ras induces heterodimerization of cRaf and BRaf.

Weber, C., Slupsky, J. R., Kalmes, H. A., & Rapp, U. R. (2001) · PubMed · Cited by 312

Allosteric Activation of Functionally Asymmetric RAF Kinase Dimers

Hu, J., Stites, E. C., Yu, H., Germino, E., Meharena, H. S., Stork, P. A., Kornev, A. P., Taylor, S. S., & Shaw, A. S. (2013) · Cell · doi:10.1016/j.cell.2013.07.046 · Cited by 303

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

Park, E., Rawson, S., Li, K., Kim, B.-W., Ficarro, S. B., Pino, G. L. G., Sharif, H., Marto, J. A., Jeon, H., & Eck, M. J. (2019) · Nature · doi:10.1038/s41586-019-1660-y · Cited by 303

Small-Molecule Modulation of Protein Homeostasis

Burslem, G. M., & Crews, C. M. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00077 · Cited by 298

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

Vasan, N., Razavi, P., Johnson, J. L., Shao, H., Shah, H., Antoine, A., Ladewig, E., Gorelick, A. N., Lin, T.-Y., Toska, E., et al. (2019) · Science · doi:10.1126/science.aaw9032 · Cited by 296

Drugs for Allosteric Sites on Receptors

Wenthur, C. J., Gentry, P. R., Mathews, T. P., & Lindsley, C. W. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134525 · Cited by 285

Protein-tyrosine kinases regulate the phosphorylation, protein interactions, subcellular distribution, and activity of p21ras GTPase-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 · Cited by 266

Conformational states dynamically populated by a kinase determine its function

Xie, T., Saleh, T., Rossi, P., & Kalodimos, C. G. (2020) · Science · doi:10.1126/science.abc2754 · Cited by 266

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

Conn, P. J., Lindsley, C. W., Meiler, J., & Niswender, C. M. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4308 · Cited by 264

Protein dynamics and allostery: an NMR view

Tzeng, S., & Kalodimos, C. G. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.10.007 · Cited by 258

NMR-based functional profiling of RASopathies and oncogenic RAS mutations

Smith, M. J., Neel, B. G., & Ikura, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218173110 · Cited by 257

Impact of linker length on the activity of PROTACs

Cyrus, K., Wehenkel, M., Choi, E.-Y., Han, H.-J., Lee, H., Swanson, H., & Kim, K.-B. (2010) · Molecular BioSystems · doi:10.1039/c0mb00074d · Cited by 232

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

Wagner, J., Lee, C. T., Durrant, J. D., Malmstrom, R. D., Feher, V. A., & Amaro, R. E. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00631 · Cited by 232

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

Raphael, B. J., Dobson, J. R., Oesper, L., & Vandin, F. (2014) · Genome Medicine · doi:10.1186/gm524 · Cited by 224

PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes

Zaidman, D., Prilusky, J., & London, N. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00589 · Cited by 224

PROTAC-DB: an online database of PROTACs

Weng, G., Shen, C., Cao, D., Gao, J., Dong, X., He, Q., Yang, B., Li, D., Wu, J., & Hou, T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa807 · Cited by 219

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

Lv, L., Chen, P., Cao, L., Li, Y., Zeng, Z., Cui, Y., Wu, Q., Li, J., Wang, J.-H., Dong, M.-Q., et al. (2020) · eLife · doi:10.7554/elife.59994 · Cited by 215

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

Burslem, G. M., Schultz, A. R., Bondeson, D. P., Eide, C. A., Savage Stevens, S. L., Druker, B. J., & Crews, C. M. (2019) · Cancer Research · doi:10.1158/0008-5472.can-19-1236 · Cited by 212

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

Barbosa, R. L., Acevedo, L. A., & Marmorstein, R. (2020) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-20-0687 · Cited by 212

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

Young, A., Lou, D., & McCormick, F. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0231 · Cited by 211

Allosteric post-translational modification codes

Nussinov, R., Tsai, C.-J., Xin, F., & Radivojac, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.07.001 · Cited by 211

GTP-Dependent K-Ras Dimerization

Muratcioglu, S., Chavan, T. S., Freed, B. C., Jang, H., Khavrutskii, L., Freed, R. N., Dyba, M. A., Stefanisko, K., Tarasov, S. G., Gursoy, A., et al. (2015) · Structure · doi:10.1016/j.str.2015.04.019 · Cited by 202

Autoregulation of the Raf-1 serine/threonine kinase

Cutler, R. E., Stephens, R. M., Saracino, M. R., & Morrison, D. K. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.16.9214 · Cited by 200

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

Fang, Z., Grütter, C., & Rauh, D. (2013) · ACS Chemical Biology · doi:10.1021/cb300663j · Cited by 197

Tissue-Specific Oncogenic Activity of KRASA146T

Poulin, E. J., Bera, A. K., Lu, J., Lin, Y.-J., Strasser, S. D., Paulo, J. A., Huang, T. Q., Morales, C., Yan, W., Cook, J., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-1220 · Cited by 197

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

Crespo, P., & León, J. (2000) · Cellular and Molecular Life Sciences · doi:10.1007/pl00000645 · Cited by 190

Allostery and population shift in drug discovery

Kar, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2010) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2010.09.002 · Cited by 190

Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view

Lu, S., Jang, H., Gu, S., Zhang, J., & Nussinov, R. (2016) · Chemical Society Reviews · doi:10.1039/c5cs00911a · Cited by 188

PI3K inhibitors: review and new strategies

Zhang, M., Jang, H., & Nussinov, R. (2020) · Chemical Science · doi:10.1039/d0sc01676d · Cited by 184

Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization

Lavoie, H., Thevakumaran, N., Gavory, G., Li, J. J., Padeganeh, A., Guiral, S., Duchaine, J., Mao, D. Y. L., Bouvier, M., Sicheri, F., et al. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1257 · Cited by 181

The Underappreciated Role of Allostery in the Cellular Network

Nussinov, R., Tsai, C., & Ma, B. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130257 · Cited by 176

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

Kondo, Y., Ognjenović, J., Banerjee, S., Karandur, D., Merk, A., Kulhanek, K. R., Wong, K., Roose, J. P., Subramaniam, S., & Kuriyan, J. (2019) · Science · doi:10.1126/science.aay0543 · Cited by 176

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

Valant, C., Lane, J. R., Sexton, P. M., & Christopoulos, A. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134514 · Cited by 174

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

Schwartz, T. W., & Holst, B. (2007) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2007.06.008 · Cited by 173

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

Michaud, N. R., Therrien, M., Cacace, A. M., Edsall, L. C., Spiegel, S., Rubin, G. M., & Morrison, D. K. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.24.12792 · Cited by 168

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

Nan, X., Collisson, E. A., Lewis, S., Huang, J., Tamgüney, T., Liphardt, J., McCormick, F. P., Gray, J. W., & Chu, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318188110 · Cited by 162

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

Rohban, M. H., Singh, S., Wu, X., Hicks‐Berthet, J., Bray, M., Shrestha, Y., Varelas, X., Boehm, J. S., & Carpenter, A. E. (2017) · eLife · doi:10.7554/elife.24060 · Cited by 162

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

Gianni, S., Freiberger, M. I., Jemth, P., Ferreiro, D. U., Wolynes, P. G., & Fuxreiter, M. (2021) · Accounts of Chemical Research · doi:10.1021/acs.accounts.0c00813 · Cited by 157

Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta

Bai, N., Miller, S. A., Andrianov, G. V., Yates, M., Kirubakaran, P., & Karanicolas, J. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c01451 · Cited by 157

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

Sun, M., Hillmann, P., Hofmann, B. T., Hart, J. R., & Vogt, P. K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009652107 · Cited by 155

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 149

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

Jenik, M., Parra, R. G., Radusky, L., Turjanski, A. G., Wolynes, P. G., & Ferreiro, D. U. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks447 · Cited by 148

A feeling for the numbers in biology

Phillips, R., & Milo, R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907732106 · Cited by 145

Computational approaches to mapping allosteric pathways

Feher, V. A., Durrant, J. D., Wart, A. T. V., & Amaro, R. E. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.02.004 · Cited by 140

Kinases and Pseudokinases: Lessons from RAF

Shaw, A. S., Kornev, A. P., Hu, J., Ahuja, L. G., & Taylor, S. S. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.00057-14 · Cited by 140

The interaction of Ras with GTPase‐activating proteins

Wittinghofer, A., Scheffzek, K., & Ahmadian, M. R. (1997) · FEBS Letters · doi:10.1016/s0014-5793(97)00321-9 · Cited by 135

Landscape and function of multiple mutations within individual oncogenes

Saito, Y., Koya, J., Araki, M., Kogure, Y., Shingaki, S., Tabata, M., McClure, M. B., Yoshifuji, K., Matsumoto, S., Isaka, Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2175-2 · Cited by 135

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

Pádua, R. A. P., Sun, Y., Marko, I., Pitsawong, W., Stiller, J. B., Otten, R., & Kern, D. (2018) · Nature Communications · doi:10.1038/s41467-018-06814-w · Cited by 133

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 133

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

Getz, G. A., Höfling, H., Mesirov, J. P., Golub, T. R., Meyerson, M. M., Tibshirani, R. J., & Lander, E. S. (2007) · Science · doi:10.1126/science.1138764 · Cited by 130

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

Tiwary, P., Mondal, J., & Berne, B. (2017) · Science Advances · doi:10.1126/sciadv.1700014 · Cited by 120

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

Predictability of human differential gene expression

Crow, M., Lim, N., Ballouz, S., Pavlidis, P., & Gillis, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1802973116 · Cited by 117

Allosteric drugs and mutations: chances, challenges, and necessity

Guarnera, E., & Berezovsky, I. N. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.01.010 · Cited by 113

The Design of Covalent Allosteric Drugs

Nussinov, R., & Tsai, C.-J. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124401 · Cited by 112

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

Terrell, E. M., Durrant, D., Ritt, D. A., Sealover, N. E., Sheffels, E., Spencer-Smith, R., Esposito, D., Zhou, Y., Hancock, J. F., Kortum, R. L., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.004 · Cited by 110

Integrated Computational Approaches and Tools for Allosteric Drug Discovery

Amamuddy, O. S., Veldman, W., Manyumwa, C. V., Khairallah, A., Agajanian, S., Odeyemi, O., Verkhivker, G. M., & Bishop, Ö. T. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21030847 · Cited by 107

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

Sträter, N., Schnappauf, G., Braus, G. H., & Lipscomb, W. N. (1997) · Structure · doi:10.1016/s0969-2126(97)00294-3 · Cited by 105

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

Nussinov, R., & Wolynes, P. G. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp90027h · Cited by 104

CABS-flex predictions of protein flexibility compared with NMR ensembles

Jamróz, M. H., Koliński, A., & Kmiecik, S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu184 · Cited by 104

Mechanistic and Structural Features of PROTAC Ternary Complexes

Casement, R., Bond, A. G., Craigon, C., & Ciulli, A. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1665-9_5 · Cited by 101

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

Xu, J., Pham, C. G., Albanese, S. K., Dong, Y., Oyama, T., Lee, C., Rodrik-Outmezguine, V. S., Yao, Z., Han, S. I., Chen, D., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci86120 · Cited by 99

Functional plasticity and evolutionary adaptation of allosteric regulation

Leander, M., Yuan, Y., Meger, A., Cui, Q., & Raman, S. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2002613117 · Cited by 98

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

Mitsis, Τ., Efthimiadou, Α., Bacopoulou, F., Vlachakis, D., Chrousos, G. P., & Eliopoulos, E. (2020) · World Academy of Sciences Journal · doi:10.3892/wasj.2020.32 · Cited by 97

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

Becher, I., Savitski, M. M., Savitski, M. F., Hopf, C., Bantscheff, M., & Drewes, G. (2012) · ACS Chemical Biology · doi:10.1021/cb3005879 · Cited by 96

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

Lu, S., Qiu, Y., Ni, D., He, X., Pu, J., & Zhang, J. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2019.10.006 · Cited by 95

Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility

Freiberger, M. I., Wolynes, P. G., Ferreiro, D. U., & Fuxreiter, M. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11068 · Cited by 95

Folding funnels and conformational transitions via hinge-bending motions

Kumar, S., Ma, B., Tsai, C.-J., Wolfson, H., & Nussinov, R. (1999) · Cell Biochemistry and Biophysics · doi:10.1007/bf02738169 · Cited by 94

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

Weerakoon, D., Carbajo, R. J., Maria, L. D., Tyrchan, C., & Zhao, H. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01036 · Cited by 94

Molecular Insights from Conformational Ensembles via Machine Learning

Fleetwood, O., Kasimova, M. A., Westerlund, A. M., & Delemotte, L. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2019.12.016 · Cited by 93

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

Bueno, A. B., Sun, B., Willard, F. S., Feng, D., Ho, J. D., Wainscott, D. B., Showalter, A. D., Vieth, M., Chen, Q., Stutsman, C., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0589-7 · Cited by 93

Allosteric Modulators: An Emerging Concept in Drug Discovery

Abdel‐Magid, A. F. (2015) · ACS Medicinal Chemistry Letters · doi:10.1021/ml5005365 · Cited by 92

Combining Allosteric and Orthosteric Drugs to Overcome Drug Resistance

Ni, D., Li, Y., Qiu, Y., Pu, J., Lu, S., & Zhang, J. (2020) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2020.02.001 · Cited by 92

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

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

Ponzoni, L., & Bahar, İ. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715896115 · Cited by 91

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

Tan, Z. W., Guarnera, E., Tee, W.-V., & Berezovsky, I. N. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa338 · Cited by 91

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

Pokrass, M. J., Ryan, K. A., Xin, T., Pielstick, B., Timp, W., Greco, V., & Regot, S. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.09.013 · Cited by 90

Rational design of allosteric modulators: Challenges and successes

Chatzigoulas, A., & Cournia, Z. (2021) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1529 · Cited by 90

Ras and the Plasma Membrane: A Complicated RelationshipPreprint

Zhou, Y., Prakash, P., Gorfe, A. A., & Hancock, J. F. (2017) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a031831 · Cited by 87

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

MA, B., KUMAR, S., TSAI, C.-J., HU, Z., & NUSSINOV, R. (2000) · Journal of Theoretical Biology · doi:10.1006/jtbi.2000.1097 · Cited by 86

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

Liang, Z. T., Verkhivker, G. M., & Hu, G. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz029 · Cited by 85

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 85

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

Ma, X., Meng, H., & Lai, L. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00039 · Cited by 83

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

Greives, N., & Zhou, H.-X. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1407545111 · Cited by 82

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

Travers, T. S., López, C. A., Van, Q. N., Neale, C., Tonelli, M., Stephen, A. G., & Gnanakaran, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-26832-4 · Cited by 82

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

Donoghue, C., Cubillos‐Rojas, M., Gutiérrez, N. M., Sánchez, C., Verdaguer, X., Riéra, A., & Nebreda, Á. R. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.112451 · Cited by 82

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

Okada, T., Hu, C., Jin, T. J., Kariya, K., Yamawaki‐Kataoka, Y., & Kataoka, T. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.9.6057 · Cited by 81

The Interdependent Activation of Son-of-Sevenless and RasPreprint

Bandaru, P., Kondo, Y., & Kuriyan, J. (2018) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a031534 · Cited by 81

Targeting RAS and PI3K in lung cancer

Downward, J. (2008) · Nature Medicine · doi:10.1038/nm1208-1315 · Cited by 80

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

Castel, P., Rauen, K. A., & McCormick, F. P. (2020) · Nature reviews. Cancer · doi:10.1038/s41568-020-0256-z · Cited by 80

Emerging Roles for AKT Isoform Preference in Cancer Progression Pathways

Degan, S. E., & Gelman, I. H. (2021) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-20-1066 · Cited by 80

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 79

How multisite phosphorylation impacts the conformations of intrinsically disordered proteins

Jin, F., & Gräter, F. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1008939 · Cited by 77

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

Li, S., Jang, H., Zhang, J., & Nussinov, R. (2018) · Structure · doi:10.1016/j.str.2018.01.011 · Cited by 76

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

Verkhivker, G. M., Agajanian, S., Hu, G., & Tao, P. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00136 · Cited by 76

Quantifying Target Occupancy of Small Molecules Within Living Cells

Robers, M. B., Ohana, R. F., Huber, K., Kilpatrick, L. E., Vasta, J. D., Berger, B., Chaudhry, C., Hill, S. J., Müller, S., Knapp, S., et al. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011420-092302 · Cited by 74

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

Fang, Z., Lee, K., Huo, K.-G., Gasmi-Seabrook, G. M. C., Zheng, L., Moghal, N., Tsao, M., Ikura, M., & Marshall, C. B. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1914076117 · Cited by 74

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

Eck, M. J., & Manley, P. W. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.01.014 · Cited by 73

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

Ye, J., Pavlı́ček, A., Lunney, E. A., Rejto, P. A., & Teng, C.-H. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-11 · Cited by 73

Inducing protein-protein interactions with molecular glues

Che, Y., Gilbert, A. M., Shanmugasundaram, V., & Noe, M. C. (2018) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2018.04.046 · Cited by 72

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

Rodrigues, T., Werner, M., Roth, J., da Cruz, E. H. G., Marques, M. C., Akkapeddi, P., Lobo, S. A. L., Koeberle, A., Corzana, F., Júnior, E. N. D. S., et al. (2018) · Chemical Science · doi:10.1039/c8sc02634c · Cited by 72

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

Allosteric Modulation of Human Hsp90α Conformational Dynamics

Penkler, D. L., Atılgan, C., & Bishop, Ö. T. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00630 · Cited by 69

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

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

Lyczek, A., Berger, B., Rangwala, A. M., Paung, Y., Tom, J., Philipose, H., Guo, J., Albanese, S. K., Robers, M. B., Knapp, S., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2111451118 · Cited by 68

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

Saleh, T., Rossi, P., & Kalodimos, C. G. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3470 · Cited by 67

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

Walker, C., Wang, Y., Olivieri, C., Karamafrooz, A., Casby, J., Bathon, K., Calebiro, D., Gao, J., Bernlohr, D., Taylor, S. S., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw9298 · Cited by 67

AlloMAPS: allosteric mutation analysis and polymorphism of signaling database

Tan, Z. W., Tee, W.-V., Guarnera, E., Booth, L., & Berezovsky, I. N. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1028 · Cited by 64

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

Signal transduction pathways involving RAS

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

Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

Marchetti, F., Moroni, E., Pandini, A., & Colombo, G. (2021) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c00045 · Cited by 62

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

Liao, J., Nie, X., Unarta, I. C., Ericksen, S. S., & Tang, W. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c02155 · Cited by 62

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

Improta-Brears, T., Ghosh, S., & Bell, R. M. (1999) · Molecular and Cellular Biochemistry · doi:10.1023/a:1006981411691 · Cited by 61

PTEN in Hereditary and Sporadic CancerPreprint

Ngeow, J. Y. Y., & Eng, C. (2019) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a036087 · Cited by 61

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

Gingell, J. J., Simms, J., Barwell, J., Poyner, D. R., Watkins, H. A., Pioszak, A. A., Sexton, P. M., & Hay, D. L. (2016) · Cell Discovery · doi:10.1038/celldisc.2016.12 · Cited by 60

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

Gao, Y., Zhou, J., Xie, Z., Wang, J., Ho, C., Zhang, Y., & Li, Q. (2019) · Communications Biology · doi:10.1038/s42003-019-0600-6 · Cited by 58

Acute depletion of CTCF rewires genome-wide chromatin accessibility

Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02466-0 · Cited by 57

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

Dixit, A., & Verkhivker, G. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026071 · Cited by 56

Precision medicine review: rare driver mutations and their biophysical classification

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · Biophysical Reviews · doi:10.1007/s12551-018-0496-2 · Cited by 56

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

Lee, Y., Phelps, C. E., Huang, T., Mostofian, B., Wu, L., Zhang, Y., Tao, K. X., Chang, Y. H., Stork, P. A., Gray, J. W., et al. (2019) · eLife · doi:10.7554/elife.46393 · Cited by 56

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

Nussinov, R., Tsai, C., & Jang, H. (2022) · Science Advances · doi:10.1126/sciadv.abm2059 · Cited by 56

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

Terai, K., & Matsuda, M. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601241 · Cited by 55

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

Acuner, S. E., Gürsoy, A., Keskin, Ö., & Nussinov, R. (2010) · PubMed · Cited by 55

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 55

Allosteric Modulators of Sigma-1 Receptor: A Review

Vavers, E., Zvejniece, L., Maurice, T., & Dambrova, M. (2019) · Frontiers in Pharmacology · doi:10.3389/fphar.2019.00223 · Cited by 54

Use of Allosteric Targets in the Discovery of Safer Drugs

Grover, A. K. (2013) · Medical Principles and Practice · doi:10.1159/000350417 · Cited by 53

Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases

Bum‐Erdene, K., Liu, D., González-Gutiérrez, G., Ghozayel, M. K., Xu, D. D., & Meroueh, S. O. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1913654117 · Cited by 53

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 53

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

Schann, S., Mayer, S., Franchet, C., Frauli, M., Steinberg, E., Thomas, M., Baron, L., & Neuville, P. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm101069m · Cited by 52

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

The structural basis for cancer treatment decisions

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

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

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

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

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

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 118

Ligand discovery by activity-based protein profiling

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