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5 results for “metadynamics”
Collective Variable for Metadynamics Derived from AlphaFold Output
<p>AlphaFold is the state of the art method for prediction of 3D structures of proteins from the amino acid sequence by neural networks. One of the outputs of AlphaFold is a probability profile of inter-residue distances for all residue pairs. We used this profile to evaluate any conformation of the studied protein to express its compliance with the AlphaFold prediction. This value can be used as a collective variable in metadynamics or parallel tempering metadynamics to accelerate protein folding in a molecular simulation. We applied this approach on folding of mini-proteins Trp-cage and beta hairpin. See V. Spiwok, M. Krečka & A. Křenek: <a href="http://doi.org/10.3389/fmolb.2022.878133">Collective Variable for Metadynamics Derived from AlphaFold Output</a> <em>Frontiers in Molecular Biosciences</em> <strong>9</strong> 878133 (2022) DOI: 10.3389/fmolb.2022.878133.</p>
Coricello et al. Metadynamics Data for WT Human ASNS (Apo Enzyme Monomer)
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Coricello et al. Metadynamics Data for WT Human ASNS (Enzyme Monomer/Aspartyl-AMP Complex)
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Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes
<p>Input scripts for the simulations</p>
Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of Binding Kinetics of Methionine Aminopeptidase-II Inhibitors
<p>Funnel-based restraint well-tempered metadynamics simulations were applied to predict residence time of two ligands bound to MetAP-II, along with ligand association and dissociation mechanism involving the identification of binding hotspot during ligands’ egressing.</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.