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11,506 results for “Dynamics”
Figure 6 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 6 Molecular dynamics of Tigogenin and Gitogenin bound to aldose reductase: (a) RMSD, (b) RMSF, (c) Hydrogen bond profile; green-Tigogenin, red-Gitogenin, black-apoprotein.
Supplementary material 1 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
List of molecular weight matched decoys retrieved from DEKOIS 2.0
Figure 5 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 5 HOMO and LUMO distribution plots: (a) HOMO (b) LUMO of Tigogenin (c) HOMO (d) LUMO of Gitogenin.
Figure 4 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 4 Intermolecular interactions of (a) Tigogenin, (b) Gitogenin, (c) Epalrestat with active-site amino acids of the enzyme aldose reductase. All the ligands are shown in all atoms' green-coloured ball and stick-type representations. The names of amino acids with ID numbers are mentioned under each circle around each ligand. On the 2D figures analysis, green-coloured dotted lines indicate hydrogen bonding interactions involving electronegative elements like nitrogen and oxygen atoms; light purple-coloured dotted lines indicate π-alkyl interactions; violet-coloured dotted lines indicate π-sigma interactions. Light green colour amino acids without bonding represent van der Waals interactions, whereas, orange-red colour amino acids indicate unfavourable interactions. The light-blue halo surrounding the interacting residues represents the solvent-accessible surface that is proportional to its diameter.
Figure 1 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 1 The binding site of aldose reductase was predicted using CASTp. The residues highlighted in blue boxes constitute the binding site.
Figure 3 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 3 Analysis and comparison of the predictive power of AutoDock and AutoDock Vina: (a) Receiver operating characteristic curves, (b) Predictiveness curves, (c) Enrichment curves, red is ADock and green is Avina.
Data From: Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
<p>This dataset contains MD simulation results for CCR5 receptor in different states. There are three states this GPCR could be in: 1.apo state, i.e. not bound to any other protein or ligand 2.holo state, i.e. bound by maraviroc (MRV) 3.GP120 bound state, i.e. bounded to HIV envelope protein GP120 and human receptor CD4. </p> <p>For apo state simulations, three different starting structure were used and the simulation results for them are given in three different folders named after the PDB ID of initial structures. </p> <p>One critical residue of CCR5 receptor, GLU283, was considered in two different protonation state, hence there are two folders for each studied system, GLU283 and GLH283 for differently protonated systems. </p> <p>The MD trajectories of studied systems are in dcd format and due to size issues waters, ions and membrane atoms were removed. </p> <p>For each system, three replica MD simulations were performed, hence, there are three folders with names REPLICA1, REPLICA2, REPLICA3.</p> <p> </p>
"Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems"
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Dataset for article titled 'Quantifying 3D time-resolved kinematics and kinetics during rapid granular compaction, Part I: quasistatic and dynamic deformation regimes'
<p>Dataset containing the raw X ray CT data, experimental XPCI images and input files for Abaqus simulations for the article titled ' Quantifying 3D time-resolved kinematics and kinetics during rapid granular compaction, Part I: quasistatic and dynamic deformation regimes' . The README file in Part1.zip provides information on the data.</p>
Data and scripts for: An analysis of the dynamic range of Distributed Acoustic Sensing for Earthquake Early Warning
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Chapter 2 - Dynamic collapse and regrowth of the Antarctic Ice Sheet in the Weddell Sea Sector during the Middle Miocene: A novel multi-proxy sedimentary provenance approach using in-situ 87Rb/87Sr dating of detrital K-feldspar - Supplementary Materials
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Data For Hybrid Monte-Carlo Molecular Dynamics Methods For Estimation of Solidus and Liquidus Compositions, a Case Study in Cu-Ni and Au-Si
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Refining species generality from a dynamical view on trophic interactions
<p>Dataset of "Refining species generality from a dynamical view on trophic interactions".</p>
Data for "Coupled cluster theory for nonadiabatic dynamics: nuclear gradients and nonadiabatic couplings in similarity constrained coupled cluster theory"
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Simulation data for "Modeling radiation belt dynamics using a positivity-preserving finite volume method on general meshes"
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Figure 6 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest
Figure 6 Proportion of leaves occupied (grey legend) or unoccupied (white legend) by phytoseiids outside the canopy (a), on adaxial side of leaves (b), red coloured phytoseiids on leaves (c), and phytoseiid on fruits (d), whenE. banksi occurred or was absent. Significant differences
Model's configuration for paper "Dynamic and Thermodynamic coupling between the Atmosphere and Ocean near the Kuroshio Current and Extension System"
<p>Here are the data used for the SKRIPS simulations. </p>
Dynamics of the gut resistome and mobilome in early life: a meta-analysis
<p>The identified marker families from CARD database (v.3.2.7) and MobileOG database (v.1.6)</p>
Picturing global substorm dynamics in the magnetotail using low-altitude ELFIN measurements and data mining-based magnetic field reconstructions (SST19 Reconstruction Output Dataset for Review)
<p>The dataset containing SST19 reconstruction output data accompanying the GRL submission for "Picturing global substorm dynamics in the magnetotail using low-altitude ELFIN measurements and data mining-based magnetic field reconstructions"</p>
The Dayside Ionosphere of Mars as controlled by the Game Between Solar Wind Dynamic Pressure and Crustal Magnetic Field Strength
<p>Including all 276 profiles like those shown in Figure 2.</p>
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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.