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Dataset results
393 results for “Molecular dynamics simulations”
Molecular dynamics simulation data of rat phenylalanine hydroxylase (rPAH) monomer
<p>Raw data of molecular dynamics simulations of rat phenylalanine hydroxylase (T22-K450) monomer. Missing residues were rebuilt using Modeller. Metal site was parameterized using MCPB.py in AmberTools. Simulation starts from the crystal pose (PDB: 5DEN).</p>
Molecular dynamics simulation data of regulatory ACT domain monomer mutation (T63P) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer mutation (T63P). Simulation setup files are also included. 21 starting conformations are used in simulations. </p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (R68S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (R68S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (T63P) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (T63P).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (L48S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (L48S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (K42I) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (K42I).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (I65T) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (I65T).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer mutation (I65S) of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer mutation (I65S).</p> <p><strong>binding.zip</strong>: simulation of dimer with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation of dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation of dimer only</p> <p>Simulation setup files are also included in each folder.</p>
Molecular Dynamics simulation of NMDA receptor TCN-213 with GluN1/2A ABD
<p>Molecular Dynamics simulation files of NMDA receptor TCN-213 with GluN1/2A ABD</p>
Identification of Potential Multi-Target Directed Ligands Through Virtual Screening and Molecular Dynamics Simulation Approach for the Treatment of Alzheimer's Disease
<p>Alzheimer’s disease (AD) is a multifactorial neurological disorder characterized by memory loss and cognitive impairment. The currently available single-targeting drugs have miserably failed in the treatment of AD and multi-target directed ligands (MTDLs) are being explored as an alternative strategy. Cholinesterase and monoamine oxidase enzymes are reported to play crucial role in the pathology of AD and multipotent ligands targeting these two enzymes simultaneously, are under various phases of design and development. Recent studies have revealed that computational approaches are robust and trusted tools for the identification of novel therapeutics. The current research work is focused on the development of potential multitarget directed ligands that simultaneously inhibit acetylcholinesterase (AChE) and monoamine oxidase B (MAO-B) enzymes employing structure-based virtual screening (SBDD) approach. The ASINEX database was screened after applying pan assay interference and drug likeness filter to identify novel molecules using three docking precision criteria Highthroughput virtual screening (HTVS), Standard Precision (SP), and extra precision (XP). Additionally, binding free energy calculations, ADME and molecular dynamic simulations were also employed to get structural insights into mechanism of protein-ligand binding and pharmacokinetic properties. Three lead molecules viz. AOP19078710, BAS00314308 and BDD26909696 were successfully identified which displayed binding score of -10.565, -10.543 & -8.066 kcal/mol against AChE and -11.019, -12.357 & -10.068 kcal/mol against MAO-B, better score as compared to the standard inhibitors. In near future, these molecules will be synthesized and evaluated through in vitro and in vivo assays for their inhibition potential against AChE and MAO-B enzymes.</p>
Data for the manuscript "Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"
<p>Simulation datasets for manuscript titled "<strong>Identification and structural studies of the crucial RNAi target of SARS-CoV-2 through molecular dynamics simulations"</strong></p>
Molecular Dynamics Simulations of four Pseudomonas aeruginosa membranes with and without Polymyxin B1
<p>This data sets contains Molecular Dynamics (MD) Simulation files of four different <em>Pseudomonas aeruginosa</em> membranes simulated with and without Polymyxin B1. Each system was simulated for 1 µs.</p> <p>The manuscript is currently under review and the data set will be published open-source after acceptance.</p>
Identification of Potential DNA Gyrase Inhibitors: Virtual Screening, Extra-Precision Docking and Molecular Dynamics Simulation Study
<p>These are the data generated during the research. All these data will be linked to the entitled work, which will be published as a research article.</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.