Citations (21)
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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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Rahul Naga, Sayan Poddar, Arghyadeep Bhattacharjee, Parimal Kar, Avishek Bose, Venkata Satish Kumar Mattaparthi, Oindrilla Mukherjee & Sougata Saha. (2023) Structural analysis of human ATE1 isoforms and their interactions with Arg-tRNAArg. Journal of Biomolecular Structure and Dynamics 0:0, pages 1-20.
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Zhipeng Tang, Yujie Ren & Fei Liu. (2022) Identify thrombin inhibitor with novel skeleton based on virtual screening study. Journal of Biomolecular Structure and Dynamics 40:1, pages 499-507.
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Zahra Khoshbin & Mohammad Reza Housaindokht. (2021) Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach. Journal of Biomolecular Structure and Dynamics 39:9, pages 3071-3079.
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Romualdo Troisi, Nicole Balasco, Luigi Vitagliano & Filomena Sica. (2021) Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites. Journal of Biomolecular Structure and Dynamics 39:6, pages 2199-2209.
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Zahra Khoshbin, Mohammad Reza Housaindokht, Mohammad Izadyar, Mohammad Reza Bozorgmehr & Asma Verdian. (2020) The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study. Journal of Biomolecular Structure and Dynamics 38:12, pages 3659-3675.
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Articles from other publishers (15)
Dizhou Wu & Freddie R. SalsburyJr.Jr.. (2023) Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods. Journal of Chemical Information and Modeling 63:12, pages 3705-3718.
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Mahroof Kalathingal & Young Min Rhee. (2023)
Molecular mechanism of binding between a therapeutic
RNA
aptamer and its protein target
VEGF
: A molecular dynamics study
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Dizhou Wu & Freddie R. SalsburyJrJr. (2022) Simulations suggest double sodium binding induces unexpected conformational changes in thrombin. Journal of Molecular Modeling 28:5.
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Romualdo Troisi, Nicole Balasco, Ida Autiero, Luigi Vitagliano & Filomena Sica. (2021) Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. International Journal of Molecular Sciences 22:19, pages 10803.
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Francesco Morena, Chiara Argentati, Ilaria Tortorella, Carla Emiliani & Sabata Martino. (2021) De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation. International Journal of Molecular Sciences 22:13, pages 6874.
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Romualdo Troisi, Nicole Balasco, Andreas Santamaria, Luigi Vitagliano & Filomena Sica. (2021) Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin. International Journal of Biological Macromolecules 181, pages 858-867.
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Ildiko M Kovach. (2021) Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System. Life 11:5, pages 396.
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Dizhou Wu, Jiajie Xiao & Freddie R. SalsburyJr.Jr.. (2021) Light Chain Mutation Effects on the Dynamics of Thrombin. Journal of Chemical Information and Modeling 61:2, pages 950-965.
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Roy González-Alemán, David Hernández-Castillo, Julio Caballero & Luis A. Montero-Cabrera. (2019) Quality Threshold Clustering of Molecular Dynamics: A Word of Caution. Journal of Chemical Information and Modeling 60:2, pages 467-472.
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Preethi Seelam Prabhakar, Richard A. Manderville & Stacey D. Wetmore. (2019) Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations. Molecules 24:16, pages 2908.
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Rebeca Miranda-Castro, Noemí de-los-Santos-Álvarez & María J. Lobo-Castañón. 2018. Aptamers for Analytical Applications. Aptamers for Analytical Applications
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Arne Krüger, Flávia Zimbres, Thales Kronenberger & Carsten Wrenger. (2018) Molecular Modeling Applied to Nucleic Acid-Based Molecule Development. Biomolecules 8:3, pages 83.
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Basri Gülbakan, Konstantin Barylyuk, Petra Schneider, Max Pillong, Gisbert Schneider & Renato Zenobi. (2018) Native Electrospray Ionization Mass Spectrometry Reveals Multiple Facets of Aptamer–Ligand Interactions: From Mechanism to Binding Constants. Journal of the American Chemical Society 140:24, pages 7486-7497.
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Hengguang Li & Grace M Chavis. (2018) Pseudo aptamer expands aptamer’s applications. MOJ Bioorganic & Organic Chemistry 2:3.
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Ryan C. Godwin, Ryan L. Melvin, William H. Gmeiner & Freddie R. SalsburyJr.Jr.. (2017) Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator). Biochemistry 56:4, pages 623-633.
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