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Original Articles

Investigation of flap flexibility of β-secretase using molecular dynamic simulations

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Pages 1008-1019 | Received 20 Mar 2015, Accepted 18 Jun 2015, Published online: 28 Jul 2015

Keep up to date with the latest research on this topic with citation updates for this article.

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Soumendranath Bhakat & Pär Söderhjelm. (2022) Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. Journal of Chemical Information and Modeling 62:4, pages 914-926.
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Samuel C. Ugbaja, Monsurat M. Lawal & Hezekiel M. Kumalo. (2022) An Overview of β-Amyloid Cleaving Enzyme 1 (BACE1) in Alzheimer's Disease Therapy: Elucidating its Exosite-Binding Antibody and Allosteric Inhibitor. Current Medicinal Chemistry 29:1, pages 114-135.
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Richa Arya, Sarvesh Paliwal, Satya P. Gupta, Swapnil Sharma, Kirtika Madan, Achal Mishra, Kanika Verma & Neha Chauhan. (2021) In-silico Studies and Biological Activity of Potential BACE-1 Inhibitors. Combinatorial Chemistry & High Throughput Screening 24:5, pages 729-736.
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Pedro R. Figueiredo, Sónia F. G. Santos, Beatriz C. Almeida, Isaura Simões & Alexandra T. P. Carvalho. (2021) Introduction of a Glycine Linker Connecting the Heavy and Light Chains in Synthetic Cardosin B-Derived Rennet Changes the Specificity of Subpocket S3′. The Journal of Physical Chemistry B 125:17, pages 4368-4374.
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Soumendranath Bhakat. (2021) Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Advances 11:18, pages 11026-11047.
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Zeynab Fakhar, Shama Khan, Suliman Y. AlOmar, Afrah Alkhuriji & Aijaz Ahmad. (2021) ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19. Scientific Reports 11:1.
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Sphelele Sosibo, Daniel Gyamfi Amoako, Anou Moise Somboro, Darren Delai Sun, Jane Catherine Ngila & Hezekiel Kumalo. (2020) Understanding the Binding Mechanism of Antagonist (AZD3293) Against BACE-1: Molecular Insights into Alzheimer’s Drug Discovery. Letters in Drug Design & Discovery 17:7, pages 850-857.
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Judite R. M. Coimbra, Salete J. Baptista, Teresa C. P. Dinis, Maria M. C. Silva, Paula I. Moreira, Armanda E. Santos & Jorge A. R. Salvador. (2020) Combining Virtual Screening Protocol and In Vitro Evaluation towards the Discovery of BACE1 Inhibitors. Biomolecules 10:4, pages 535.
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Raitis Bobrovs, Kristaps Jaudzems & Aigars Jirgensons. (2019) Exploiting Structural Dynamics To Design Open-Flap Inhibitors of Malarial Aspartic Proteases. Journal of Medicinal Chemistry 62:20, pages 8931-8950.
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Nalini Schaduangrat, Veda Prachayasittikul, Saowapak Choomwattana, Prapimpun Wongchitrat, Kamonrat Phopin, Wilasinee Suwanjang, Aijaz Ahmad Malik, Bruno Vincent & Chanin Nantasenamat. (2019) Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease. Medicinal Research Reviews 39:5, pages 1730-1778.
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Akhil Kumar & Ashok Sharma. 2018. Computational Modeling of Drugs Against Alzheimer’s Disease. Computational Modeling of Drugs Against Alzheimer’s Disease 533 571 .
Lara McGillewie, Muthusamy Ramesh & Mahmoud E. Soliman. (2017) Sequence, Structural Analysis and Metrics to Define the Unique Dynamic Features of the Flap Regions Among Aspartic Proteases. The Protein Journal 36:5, pages 385-396.
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Carlos Gueto-Tettay, Alejandro Martinez-Consuegra, Joshua Zuchniarz, Luis Roberto Gueto-Tettay & Juan Carlos Drosos-Ramírez. (2017) A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process. Journal of Molecular Graphics and Modelling 76, pages 274-288.
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Sergio M. Marques, Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jan Brezovsky & Jiri Damborsky. (2017) Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Medicinal Research Reviews 37:5, pages 1095-1139.
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Ornella Di Pietro, Jordi Juárez-Jiménez, Diego Muñoz-Torrero, Charles A. Laughton & F. Javier Luque. (2017) Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors. PLOS ONE 12:5, pages e0177683.
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Zeynab Fakhar, Thavendran Govender, Glenn E. M. Maguire, Gyanu Lamichhane, Ross C. Walker, Hendrik G. Kruger & Bahareh Honarparvar. (2017) Differential flap dynamics in l , d -transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics . Molecular BioSystems 13:6, pages 1223-1234.
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Carlos Gueto-Tettay, Joshua Zuchniarz, Yeyson Fortich-Seca, Luis Roberto Gueto-Tettay & Juan Carlos Drosos-Ramirez. (2016) A molecular dynamics study of the BACE1 conformational change from Apo to closed form induced by hydroxyethylamine derived compounds. Journal of Molecular Graphics and Modelling 70, pages 181-195.
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Rajiv K. Bedi, Chandan Patel, Vandana Mishra, Huogen Xiao, Rickey Y. Yada & Prasenjit Bhaumik. (2016) Understanding the structural basis of substrate recognition by Plasmodium falciparum plasmepsin V to aid in the design of potent inhibitors. Scientific Reports 6:1.
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