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Journal of Biomolecular Structure and Dynamics Volume 38, 2020 - Issue 6
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Research Articles

Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation

Abdullahi Ibrahim UbaDepartment of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey;
,
Jackson WeakoComputational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
,
Özlem KeskinComputational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
,
Attila GürsoyComputational Biology and Bioinformatics Department, Faculty of Science and Engineering, Koç University, Sariyer/Istanbul, Turkey
&
Kemal YelekçiDepartment of Bioinformatics and Genetics, Faculty of Engineering and Natural Science, Kadir Has University, Istanbul, Turkey; Correspondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-0052-4926
ORCID Icon
Pages 1751-1760 | Received 12 Apr 2019, Accepted 01 May 2019, Published online: 20 May 2019

Citations (11)

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Balaji Wamanrao Matore, Partha Pratim Roy & Jagadish Singh. (2023) Discovery of novel VEGFR2-TK inhibitors by phthalimide pharmacophore based virtual screening, molecular docking, MD simulation and DFT. Journal of Biomolecular Structure and Dynamics 41:22, pages 13056-13077.
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Guoyi Yan, Dongxiao Li, Xinxin Zhong, Ge Liu, Xueqin Wang, Yuanxiang Lu, Fangyuan Qin, Yuqi Guo, Shaofeng Duan & Deyu Li. (2021) Identification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics 39:6, pages 1928-1939.
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Abdullahi Ibrahim Uba & Kemal Yelekçi. (2020) Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10. Journal of Biomolecular Structure and Dynamics 38:15, pages 4397-4406.
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Articles from other publishers (8)

José Eduardo Guzmán Ramírez & Teresa Mancilla Percino. (2023) Synthesis of N‐aminophalimides derived from α‐amino acids: Theoretical study to find them as HDAC8 inhibitors by docking simulations and in vitro assays . Chemical Biology & Drug Design 102:6, pages 1367-1386.
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Abdullahi Ibrahim Uba & Gokhan Zengin. (2023) In the quest for histone deacetylase inhibitors: current trends in the application of multilayered computational methods. Amino Acids.
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Anna Fontana, Ilaria Cursaro, Gabriele Carullo, Sandra Gemma, Stefania Butini & Giuseppe Campiani. (2022) A Therapeutic Perspective of HDAC8 in Different Diseases: An Overview of Selective Inhibitors. International Journal of Molecular Sciences 23:17, pages 10014.
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Abdullahi Ibrahim Uba & Chun Wu. (2022) Identification of potential antagonists of CRF1R for possible treatment of stress and anxiety neuro-disorders using structure-based virtual screening and molecular dynamics simulation. Computational Biology and Chemistry, pages 107743.
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Safana Albayati, Abdullahi Ibrahim Uba & Kemal Yelekçi. (2021) Potential inhibitors of methionine aminopeptidase type II identified via structure-based pharmacophore modeling. Molecular Diversity 26:2, pages 1005-1016.
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Minal Mahajan, Snehal Suryavanshi, Shovonlal Bhowmick, Fatmah Ali Alasmary, Tahani Mazyad Almutairi, Md Ataul Islam & Ruchika Kaul-Ghanekar. (2021) Matairesinol, an active constituent of HC9 polyherbal formulation, exhibits HDAC8 inhibitory and anticancer activity. Biophysical Chemistry 273, pages 106588.
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Yudibeth Sixto-López & José Correa-Basurto. 2021. Molecular Docking for Computer-Aided Drug Design. Molecular Docking for Computer-Aided Drug Design 367 390 .
Neha Upadhyay, Kalpana Tilekar, Niklas Jänsch, Markus Schweipert, Jessica D. Hess, Luca Henze Macias, Piotr Mrowka, Renato J. Aguilera, Jun-yong Choe, Franz-Josef Meyer-Almes & C.S. Ramaa. (2020) Discovery of novel N-substituted thiazolidinediones (TZDs) as HDAC8 inhibitors: in-silico studies, synthesis, and biological evaluation. Bioorganic Chemistry 100, pages 103934.
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