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691 results for “Molecular dynamics”
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>
Supplementary molecular docking and dynamics data of poxin inhibitors of mpox
Open the record for dataset details and reuse information.
Alternatively-spliced isoforms of the cardiac Nav1.5 sodium channel modify channel activation by distinct structural mechanisms - Molecular dynamics results
<p>Output files associated with molecular dynamics simulations of the alternative splice variant of Nav1.5</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>
Molecular dynamics trajectories for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity"
<p>Dataset of molecular dynamics trajectories obtained for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity"</p> <p>Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, and increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in the VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (alpha, beta, delta, and omicron). Our results show that, in solution, wt RBD presents two distinct conformations: an “open” conformation where it is free to bind ACE2; and a “closed” conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the delta and omicron variants showed extreme results, with the closed conformation either barely observed or not observed at all. The delta variant also differed from the other variants substantially, alternating between the open conformation and an alternative “reversed” one, with a significantly changed orientation of the RBM ridge. This alternate conformation could potentially provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the omicron and delta variant, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of delta, antibody escape.</p>
Structural distortion of β-cyclodextrin plays a key role for the pH-dependent host-guest chemistry with doxorubicin, evident by electrochemical and molecular dynamics approach
<p>β-cyclodextrin (β-CD) is the potential drug carrier to deliver antitumor drugs like doxorubicin<br> (DOX). However, the mechanism for the inclusion complex formation is still unclear and<br> needs to be explored. This study investigated the effect of pH on the inclusion of DOX into<br> thiolated β-CD (β-CD-SH) by electrochemical and molecular dynamics (MD) simulation.<br> The electrochemical study shows a clear difference at different pH. The redox peak due to the<br> DOX is strongly influenced by pH. At neutral pH, the peak intensity decreases with time,<br> while slight variation is observed at acidic and basic pH. Depicting the association of DOX to<br> the β-CD-SH cavity at neutral pH. Also, due to the association, the charge transfer resistance<br> variation increased with time at neutral pH, decreased at basic and acidic pH. The<br> electrochemical study was further supported by MD simulation, suggesting that the<br> cyclodextrins ring gets slightly elongated due to the flipping of glucose units,<br> specifically at neutral pH leads to a strong association. Also, another significant result<br> observed that the DOX forms an inclusion complex with β-CD-SH in quinol conformation,<br> not in quinone. Briefly, the study provides the necessary molecular binding information for<br> designing an effective β-CD based targeted drug delivery system.</p>
Phytochemicals from AYUSH-64 screened against main protease and spike protein of Omicron variant of SARS-CoV-2 using ensemble docking and molecular dynamics approach
<p>Data for "Phytochemicals from AYUSH-64 screened against main protease and spike protein of Omicron variant of SARS-CoV-2 using ensemble docking and molecular dynamics approach" </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.