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For: Lu S, He X, Yang Z, Chai Z, Zhou S, Wang J, Rehman AU, Ni D, Pu J, Sun J, Zhang J. Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nat Commun 2021;12:4721. [PMID: 34354057 DOI: 10.1038/s41467-021-25020-9] [Cited by in Crossref: 56] [Cited by in F6Publishing: 58] [Article Influence: 28.0] [Reference Citation Analysis]
Number Citing Articles
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6 Li X, Li B, Li J, Yang M, Bai Y, Chen K, Chen Z, Mao N. Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase. Front Mol Biosci 2022;9:1104942. [PMID: 36601586 DOI: 10.3389/fmolb.2022.1104942] [Reference Citation Analysis]
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9 Heo L, Feig M. Multi-state modeling of G-protein coupled receptors at experimental accuracy. Proteins 2022;90:1873-85. [PMID: 35510704 DOI: 10.1002/prot.26382] [Cited by in Crossref: 12] [Cited by in F6Publishing: 12] [Article Influence: 12.0] [Reference Citation Analysis]
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11 Torino S, Dhurandhar M, Stroobants A, Claessens R, Efremov RG. Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting.. [DOI: 10.1101/2022.10.21.513149] [Reference Citation Analysis]
12 Song S, Shao Z. From Myricetin to the Discovery of Novel Natural Human ENPP1 Inhibitors: A Virtual Screening, Molecular Docking, Molecular Dynamics Simulation, and MM/GBSA Study. Molecules 2022;27:6175. [DOI: 10.3390/molecules27196175] [Reference Citation Analysis]
13 Zheng G, Li M, Zhang J, Liu W, Jiang L, Liang W, Wang J, Shi H, Kang Z, Zhou B. A computational study to reveal selpercatinib resistance to RET kinase double mutant V804M/Y806C. Chem Pap . [DOI: 10.1007/s11696-022-02479-4] [Reference Citation Analysis]
14 Wang G, Bai Y, Cui J, Zong Z, Gao Y, Zheng Z. Computer-Aided Drug Design Boosts RAS Inhibitor Discovery. Molecules 2022;27:5710. [PMID: 36080477 DOI: 10.3390/molecules27175710] [Reference Citation Analysis]
15 Zhang H, Chu G, Wang G, Yao M, Lu S, Chen T. Mechanistic Understanding of the Palmitoylation of Go Protein in the Allosteric Regulation of Adhesion Receptor GPR97. Pharmaceutics 2022;14:1856. [PMID: 36145604 DOI: 10.3390/pharmaceutics14091856] [Reference Citation Analysis]
16 Persechino M, Hedderich JB, Kolb P, Hilger D. Allosteric modulation of GPCRs: From structural insights to in silico drug discovery. Pharmacology & Therapeutics 2022;237:108242. [DOI: 10.1016/j.pharmthera.2022.108242] [Reference Citation Analysis]
17 Aplin C, Milano SK, Zielinski KA, Pollack L, Cerione RA. Evolving Experimental Techniques for Structure-Based Drug Design. J Phys Chem B 2022. [PMID: 36029222 DOI: 10.1021/acs.jpcb.2c04344] [Reference Citation Analysis]
18 Zhang H, Ni D, Fan J, Li M, Zhang J, Hua C, Nussinov R, Lu S. Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation. J Chem Inf Model 2022. [PMID: 35994329 DOI: 10.1021/acs.jcim.2c00591] [Reference Citation Analysis]
19 Portilla-martínez A, Ortiz-flores MÁ, Meaney E, Villarreal F, Nájera N, Ceballos G. (-)-Epicatechin Is a Biased Ligand of Apelin Receptor. IJMS 2022;23:8962. [DOI: 10.3390/ijms23168962] [Reference Citation Analysis]
20 Zhuang H, Fan J, Li M, Zhang H, Yang X, Lin L, Lu S, Wang Q, Liu Y. Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C. Front Oncol 2022;12:915512. [DOI: 10.3389/fonc.2022.915512] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
21 Zhou S, Yang B, Xu Y, Gu A, Peng J, Fu J. Understanding gilteritinib resistance to FLT3-F691L mutation through an integrated computational strategy. J Mol Model 2022;28:247. [PMID: 35932378 DOI: 10.1007/s00894-022-05254-0] [Reference Citation Analysis]
22 Li M, Wang Y, Fan J, Zhuang H, Liu Y, Ji D, Lu S. Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading. J Mol Biol 2022;:167730. [PMID: 35872068 DOI: 10.1016/j.jmb.2022.167730] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
23 Liu C, Zhang Y, Zhang Y, Liu Z, Mao F, Chai Z. Mechanistic Insights into the Mechanism of Inhibitor Selectivity toward the Dark Kinase STK17B against Its High Homology STK17A. Molecules 2022;27:4655. [DOI: 10.3390/molecules27144655] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
24 Wang A, Durrant JD. Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery. Molecules 2022;27:4623. [DOI: 10.3390/molecules27144623] [Reference Citation Analysis]
25 Tripathy M, Srivastava A, Sastry S, Rao M. Protein as evolvable functionally-constrained amorphous matter.. [DOI: 10.1101/2022.07.17.500335] [Reference Citation Analysis]
26 Shi Y, Cao S, Ni D, Fan J, Lu S, Xue M. The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor. Front Mol Biosci 2022;9:933676. [DOI: 10.3389/fmolb.2022.933676] [Reference Citation Analysis]
27 Ji M, Chai Z, Chen J, Li G, Li Q, Li M, Ding Y, Lu S, Ju G, Hou J. Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study. Molecules 2022;27:4149. [DOI: 10.3390/molecules27134149] [Reference Citation Analysis]
28 Mishra D, Mishra A, Katara P, Singh MP. In silico identification of potential inhibitors of MPS1 from edible mushroom (Pleurotus ostreatus) to prevent aneuploidy and tumorigenesis. J Proteins Proteom 2022;13:175-185. [DOI: 10.1007/s42485-022-00091-4] [Reference Citation Analysis]
29 Mitgau J, Franke J, Schinner C, Stephan G, Berndt S, Placantonakis DG, Kalwa H, Spindler V, Wilde C, Liebscher I. The N Terminus of Adhesion G Protein–Coupled Receptor GPR126/ADGRG6 as Allosteric Force Integrator. Front Cell Dev Biol 2022;10:873278. [DOI: 10.3389/fcell.2022.873278] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
30 Dixon AD, Trinidad JC, Ziarek JJ. A Method for Selective 19F-Labeling Absent of Probe Sequestration (SLAPS).. [DOI: 10.1101/2022.06.17.496653] [Reference Citation Analysis]
31 Diberto JF, Smart K, Olsen RH, Roth BL. Agonist and antagonist TRUPATH assays for G protein-coupled receptors. STAR Protocols 2022;3:101259. [DOI: 10.1016/j.xpro.2022.101259] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
32 Yang X, Wang X, Xu Z, Wu C, Zhou Y, Wang Y, Lin G, Li K, Wu M, Xia A, Liu J, Cheng L, Zou J, Yan W, Shao Z, Yang S. Molecular mechanism of allosteric modulation for the cannabinoid receptor CB1. Nat Chem Biol. [DOI: 10.1038/s41589-022-01038-y] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
33 Cong X, Zhang X, Liang X, He X, Tang Y, Zheng X, Lu S, Zhang J, Chen T. Delineating the conformational landscape and intrinsic properties of the angiotensin II type 2 receptor using a computational study. Comput Struct Biotechnol J 2022;20:2268-79. [PMID: 35615027 DOI: 10.1016/j.csbj.2022.05.012] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
34 Hedderich JB, Persechino M, Becker K, Heydenreich FM, Gutermuth T, Bouvier M, Bünemann M, Kolb P. The pocketome of G-protein-coupled receptors reveals previously untargeted allosteric sites. Nat Commun 2022;13:2567. [PMID: 35538063 DOI: 10.1038/s41467-022-29609-6] [Cited by in Crossref: 4] [Cited by in F6Publishing: 6] [Article Influence: 4.0] [Reference Citation Analysis]
35 Liu C, Li Z, Liu Z, Yang S, Wang Q, Chai Z. Understanding the P-Loop Conformation in the Determination of Inhibitor Selectivity Toward the Hepatocellular Carcinoma-Associated Dark Kinase STK17B. Front Mol Biosci 2022;9:901603. [DOI: 10.3389/fmolb.2022.901603] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
36 Mo P, Li C, Zhao D, Zhang Y, Shi M, Li J, Liu J. Accurate and efficient molecular dynamics based on machine learning and non von Neumann architecture. npj Comput Mater 2022;8. [DOI: 10.1038/s41524-022-00773-z] [Reference Citation Analysis]
37 Cruz MA, Frederick TE, Mallimadugula UL, Singh S, Vithani N, Zimmerman MI, Porter JR, Moeder KE, Amarasinghe GK, Bowman GR. A cryptic pocket in Ebola VP35 allosterically controls RNA binding. Nat Commun 2022;13:2269. [PMID: 35477718 DOI: 10.1038/s41467-022-29927-9] [Reference Citation Analysis]
38 Parray ZA, Shahid M, Islam A. Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological Functions. Polymers (Basel) 2022;14:1539. [PMID: 35458289 DOI: 10.3390/polym14081539] [Reference Citation Analysis]
39 He X, Du K, Wang Y, Fan J, Li M, Ni D, Lu S, Bian X, Liu Y. Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Front Mol Biosci 2022;9:860962. [DOI: 10.3389/fmolb.2022.860962] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 6.0] [Reference Citation Analysis]
40 Wang CX, Wang TT, Zhang KD, Li MY, Shen QC, Lu SY, Zhang J. Pan-KRAS inhibitors suppress proliferation through feedback regulation in pancreatic ductal adenocarcinoma. Acta Pharmacol Sin 2022. [PMID: 35352018 DOI: 10.1038/s41401-022-00897-4] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
41 Mozumder S, Bej A, Sengupta J. Ligand-Dependent Modulation of the Dynamics of Intracellular Loops Dictates Functional Selectivity of 5-HT2AR. J Chem Inf Model 2022. [PMID: 35324173 DOI: 10.1021/acs.jcim.2c00118] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
42 Dokainish HM, Re S, Mori T, Kobayashi C, Jung J, Sugita Y. The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. Elife 2022;11:e75720. [PMID: 35323112 DOI: 10.7554/eLife.75720] [Cited by in Crossref: 8] [Cited by in F6Publishing: 8] [Article Influence: 8.0] [Reference Citation Analysis]
43 Singh KD, Karnik SS. Structural perspectives on the mechanism of signal activation, ligand selectivity and allosteric modulation in angiotensin receptors: IUPHAR Review 34. Br J Pharmacol 2022. [PMID: 35318654 DOI: 10.1111/bph.15840] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
44 Xu M, li Y, Dong J, Yuan S. GPCR-IFP: A Web Server for Analyzing G-Protein Coupled Receptor-Ligand Fingerprint Interaction from Experimental Structures.. [DOI: 10.1101/2022.03.16.484667] [Reference Citation Analysis]
45 Ni D, Liu Y, Kong R, Yu Z, Lu S, Zhang J. Computational elucidation of allosteric communication in proteins for allosteric drug design. Drug Discovery Today 2022. [DOI: 10.1016/j.drudis.2022.03.012] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
46 Zhuang H, Fan X, Ji D, Wang Y, Fan J, Li M, Ni D, Lu S, Li X, Chai Z. Elucidation of the conformational dynamics and assembly of Argonaute−RNA complexes by distinct yet coordinated actions of the supplementary microRNA. Computational and Structural Biotechnology Journal 2022. [DOI: 10.1016/j.csbj.2022.03.001] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 5.0] [Reference Citation Analysis]
47 Shen D, Liu H, Qian F, Wang P. Design, synthesis and evaluation of novel thienopyridazine derivatives as Chk1/2 inhibitors. Bioorg Chem 2022;121:105704. [PMID: 35240418 DOI: 10.1016/j.bioorg.2022.105704] [Reference Citation Analysis]
48 Van Baelen A, Robin P, Kessler P, Maïga A, Gilles N, Servent D. Structural and Functional Diversity of Animal Toxins Interacting With GPCRs. Front Mol Biosci 2022;9:811365. [DOI: 10.3389/fmolb.2022.811365] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
49 Arantes PR, Patel AC, Palermo G. Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids. Journal of Molecular Biology 2022. [DOI: 10.1016/j.jmb.2022.167518] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
50 Zha J, Li M, Kong R, Lu S, Zhang J. Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques. Journal of Molecular Biology 2022. [DOI: 10.1016/j.jmb.2022.167481] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
51 Liang S, Wang Q, Qi X, Liu Y, Li G, Lu S, Mou L, Chen X. Deciphering the Mechanism of Gilteritinib Overcoming Lorlatinib Resistance to the Double Mutant I1171N/F1174I in Anaplastic Lymphoma Kinase. Front Cell Dev Biol 2021;9:808864. [PMID: 35004700 DOI: 10.3389/fcell.2021.808864] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 7.0] [Reference Citation Analysis]
52 Wang Y, Li M, Liang W, Shi X, Fan J, Kong R, Liu Y, Zhang J, Chen T, Lu S. Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor. Computational and Structural Biotechnology Journal 2022;20:628-39. [DOI: 10.1016/j.csbj.2022.01.015] [Cited by in Crossref: 15] [Cited by in F6Publishing: 16] [Article Influence: 15.0] [Reference Citation Analysis]
53 Abrol R, Serrano E, Santiago LJ. Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs. Membrane Proteins 2022. [DOI: 10.1016/bs.apcsb.2021.11.001] [Reference Citation Analysis]
54 Diberto JF, Olsen RHJ, Roth BL. TRUPATH: An Open-Source Biosensor Platform for Interrogating the GPCR Transducerome. Bioluminescence 2022. [DOI: 10.1007/978-1-0716-2473-9_13] [Reference Citation Analysis]
55 Fan J, Liu Y, Kong R, Ni D, Yu Z, Lu S, Zhang J. Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. J Med Chem 2021;64:17728-43. [PMID: 34878270 DOI: 10.1021/acs.jmedchem.1c01695] [Cited by in Crossref: 12] [Cited by in F6Publishing: 12] [Article Influence: 6.0] [Reference Citation Analysis]
56 Li X, Wang C, Peng T, Chai Z, Ni D, Liu Y, Zhang J, Chen T, Lu S. Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Comput Struct Biotechnol J 2021;19:6108-24. [PMID: 34900128 DOI: 10.1016/j.csbj.2021.11.010] [Cited by in Crossref: 23] [Cited by in F6Publishing: 23] [Article Influence: 11.5] [Reference Citation Analysis]
57 Heo L, Feig M. Multi-State Modeling of G-protein Coupled Receptors at Experimental Accuracy.. [DOI: 10.1101/2021.11.26.470086] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
58 Cao S, Jiang X, Tan C, Fu M, Xiong W, Ji D, Lv J. How does nintedanib overcome cancer drug-resistant mutation of RET protein-tyrosine kinase: insights from molecular dynamics simulations. J Mol Model 2021;27:337. [PMID: 34725737 DOI: 10.1007/s00894-021-04964-1] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
59 Ni D, Chai Z, Wang Y, Li M, Yu Z, Liu Y, Lu S, Zhang J. Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. WIREs Comput Mol Sci. [DOI: 10.1002/wcms.1585] [Cited by in Crossref: 9] [Cited by in F6Publishing: 11] [Article Influence: 4.5] [Reference Citation Analysis]
60 Lymperopoulos A, Borges JI, Carbone AM, Cora N, Sizova A. Cardiovascular angiotensin II type 1 receptor biased signaling: Focus on non-Gq-, non-βarrestin-dependent signaling. Pharmacol Res 2021;174:105943. [PMID: 34662735 DOI: 10.1016/j.phrs.2021.105943] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
61 Tamura K, Azushima K, Kinguchi S, Wakui H, Yamaji T. ATRAP, a receptor-interacting modulator of kidney physiology, as a novel player in blood pressure and beyond. Hypertens Res 2021. [PMID: 34642449 DOI: 10.1038/s41440-021-00776-1] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
62 Li X, Qi Z, Ni D, Lu S, Chen L, Chen X. Markov State Models and Molecular Dynamics Simulations Provide Understanding of the Nucleotide-Dependent Dimerization-Based Activation of LRRK2 ROC Domain. Molecules 2021;26:5647. [PMID: 34577121 DOI: 10.3390/molecules26185647] [Cited by in Crossref: 9] [Cited by in F6Publishing: 9] [Article Influence: 4.5] [Reference Citation Analysis]
63 Zheng G, Xu S, Liu W, Du T, Zhang J, Li M, Cai C, Shi H. Deciphering the resistance mechanism of RET kinase mutant against vandetanib and nintedanib using molecular dynamics simulations. Journal of Experimental Nanoscience 2021;16:278-93. [DOI: 10.1080/17458080.2021.1970141] [Cited by in Crossref: 1] [Article Influence: 0.5] [Reference Citation Analysis]
64 Nejat R, Sadr AS, Torshizi MF, Najafi DJ. GPCRs of Diverse Physiologic and Pathologic Effects with Fingerprints in COVID-19. ECB 2021 2021. [DOI: 10.3390/ecb2021-10261] [Reference Citation Analysis]