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53 results for “docking simulations”
Fig. 6. Molecular docking simulation. A in In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect
Fig. 6. Molecular docking simulation. A) root-mean-square deviation (RMSD) B) number of hydrogen bonds C) radius of gyration D) minimum distance of OC XI – cathepsin O2 like and OC V – cathepsin F like complexes. Red color line denotes OC V- cathepsin F like and black color line denotes OC XI- cathepsin O2 like. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4. 3D docking simulations and 2D in Meroterpenoids from the leaves of Psidium guajava (guava) cultivated in Korea using MS/MS-based molecular networking
Fig. 4. 3D docking simulations and 2D diagrams of ligand interactions for compounds 1–4 in the active site of PTP1B (PDB code 1NNY).
Identification of novel NLRP3 Inhibitors a comprehensive approach using 2D-QSAR, molecular docking, molecular dynamics simulation and drug-likeness evaluation
<p>This dataset encapsulates the comprehensive outputs derived from molecular docking and molecular dynamics (MD) simulation studies conducted to investigate the binding affinities, interactions, and dynamic behaviors of selected ligands with NLRP3.</p>
Figure 4 from: Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
Figure 4 Number of HBs and RMSD between N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with three flavones 428, 581, and 864 (Fig. A–C, respectively) during dynamic simulation time 500 ns.
Figure 5 from: Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
Figure 5 The proposed semi-synthesis of compound 864. (i) Column chromatography (70% EtOH: 18.64 mg.g−1) (ii) ClCH2COCl, K2CO3, DCM, rt, 8–24h; (iii) K2CO3/KI, acetone, reflux, 25–30 h.
Figure 2 from: Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
Figure 2 2D interaction diagrams and 3D molecular docking of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with four flavones 428, 581, 864, and 948 (A–D, respectively) and two flavonols 162 and 218, (E, F, respectively).
Figure 3 from: Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
Figure 3 3D molecular docking of bifunctional N inhibitor (compound 864) binding into the sialic acid binding cavity and the 430-cavity through the unique arginine triad Arg118-Arg292-Arg371 of N1-H274Y-oseltamivir protein (PDB ID: 3CL0).
Figure 1 from: Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
Figure 1 Procedure of molecular docking screening and molecular dynamics of flavones and flavonols from COCONUT database.
Supplementary material 1 from: Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
Supporting data
In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer's disease
<p>We added Supplementary Figure 8a.</p>
Figure 7 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 7 2D poses of (A) Mesuol; (B) Isomesuol; (C) suksdorphin; (D) Calanolide; docked into the active site of SARS-CoV-2 main protease (PDB: 5rh4).
Figure 6 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 6 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin docked into the active site of SARS-CoV-2 main protease (PDB: 5rh4).
Figure 12 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 12 The time frame of evolution against the radius of gyration (Rg) of Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, during 50 ns MD simulation.
Figure 11 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 11 The RMSF plot of Coumermycin complex with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, at 50 ns simulation.
Figure 5 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 5 2D poses of (A) Novobiocin; (C) Clorobiocin; (B) hydroxychloroquine; (D) N3; docked into the active site of SARS-CoV-2 main protease.
Figure 9 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 9 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 RNA-dependent RNA polymerase (PDB: 7bv2).
Figure 4 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 4 (A) Structure of standard inhibitor of SARS-CoV-2 main protease, N3, (B) 2D pose for the interaction of hydroxychloroquine into the active site of SARS-Cov-2 main protease enzyme.
Figure 8 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 8 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 papain-like protease (PDB: 6wx4).
Figure 10 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 10 The RMSD plot of Coumermycin complex with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, at 50 ns simulation.
Figure 13 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Figure 13 The time frame of evolution against SASA of Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, during 50 ns simulation.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.