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Research Article

Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses

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Pages 373-398 | Received 15 Jan 2020, Accepted 24 Mar 2020, Published online: 04 Jun 2020

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Lifei Wang, Dan Lu, Yan Wang, Xiaoyan Xu, Peihua Zhong & Zhiyong Yang. (2023) Binding selectivity-dependent molecular mechanism of inhibitors towards CDK2 and CDK6 investigated by multiple short molecular dynamics and free energy landscapes. Journal of Enzyme Inhibition and Medicinal Chemistry 38:1, pages 84-99.
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Manasi Yadav, Mohnad Abdalla, Maddala Madhavi, Ishita Chopra, Anushka Bhrdwaj, Lovely Soni, Uzma Shaheen, Leena Prajapati, Megha Sharma, Mayank Singh Sikarwar, Sarah Albogami, Tajamul Hussain, Anuraj Nayarisseri & Sanjeev Kumar Singh. (2022) Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. Molecular Simulation 48:12, pages 1081-1101.
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D. Luo, J.B. Tong, X.C. Xiao, S. Bian, X. Zhang, J. Wang & H.Y. Xu. (2021) Theoretically exploring selective-binding mechanisms of BRD4 through integrative computational approaches. SAR and QSAR in Environmental Research 32:12, pages 985-1011.
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Y.X. Yu, W.T. Liu, H.Y. Li, W. Wang, H.B. Sun, L.L. Zhang & S.L. Wu. (2021) Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations. SAR and QSAR in Environmental Research 32:11, pages 889-915.
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S.S. Liang, X.G. Liu, Y.X. Cui, S.L. Zhang, Q.G. Zhang & J.Z. Chen. (2021) Molecular mechanism concerning conformational changes of CDK2 mediated by binding of inhibitors using molecular dynamics simulations and principal component analysis. SAR and QSAR in Environmental Research 32:7, pages 573-594.
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Y.Y. Yin, J. Zhao, L.L. Zhang, X.Y. Xu & J.Q. Liu. (2021) Molecular mechanisms of inhibitor bindings to A-FABP deciphered by using molecular dynamics simulations and calculations of MM-GBSA. SAR and QSAR in Environmental Research 32:4, pages 293-315.
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S.L. Wu, J. Zhao, H.B. Sun, H.Y. Li, Y.Y. Yin & L.L. Zhang. (2021) Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations. SAR and QSAR in Environmental Research 32:3, pages 221-246.
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Articles from other publishers (2)

Lifei Wang, Yan Wang, Zhiyong Yang, Shuobo Xu & Hongyun Li. (2021) Binding Selectivity of Inhibitors toward Bromodomains BAZ2A and BAZ2B Uncovered by Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations. ACS Omega 6:18, pages 12036-12049.
Crossref
Yan Wang, Shiliang Wu, Lifei Wang, Zhiyong Yang, Juan Zhao & Lulu Zhang. (2021) Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations. RSC Advances 11:2, pages 745-759.
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