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ShareScore release 0.9.0
Dataset results
3 results for “molecular dissociation”
Molecular Dynamic Simulation on the Role of CL5D in Accelerate the Product Dissociation of SIRT6
<p>The source data used to generate figures in the main text is stored in the ‘Source Data.xlsx’ file, and 'Source Data Description.docx' is a brief description of the source data table.<br>'SIRT6.prmtop' and 'SIRT6.inpcrd' are initial structure of SIRT6 system,'SIRT6-CL5D.prmtop' and 'SIRT6-CL5D.inpcrd' are initial structure of SIRT6-CL5D system.<br>'SIRT6_equ.pdb', 'SIRT6-CL5D'_equ.pdb are snapshots of the equilibrium structure of the SIRT6 system and the SIRT6-CL5D system, respectively.<br>'ramd.conf' is an example configuration file that uses RAMD simulations to obtain the AR6 dissociation path in the SIRT6 system, with the acceleration of 0.0625 kcal/Å/g and a cutoff distance of 0.005 Å.<br>'win1.conf' and 'win1.in' are example configuration files for the first window of the umbrella sampling, which calculates the dissociation energy barrier of AR6 in the SIRT6 system,'win1.in' is the parameter file for umbrella sampling, with A 2.5 kcal/mol/Ų spring constant, and window center is 9 Å.</p> <p> </p>
A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories
<p>Containes input data for MD simulations of 3 HSP90- small compound complexes from the paper</p> <p>A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories" from Daria B. Kokh, Bernd Doser , Stefan Richter , Fabian Ormersbach , Xingyi Cheng, Rebecca C. Wade, publishe in J. Chem. Phys. <strong>153</strong>, 125102 (2020); <a href="https://doi.org/10.1063/5.0019088">https://doi.org/10.1063/5.0019088</a></p> <ul> <li>ref.pdb - structure of the complex in PDB format</li> <li>ref.prmtop - topology file in AMBER</li> <li>ref-equal-NTP.pdb - structure after NTP equilibration </li> <li>ref-equal-NTP.rst7 - coordinates after NTP equilibration</li> <li>ref-equal-NTP.crd - coordinates after NTP equilibration </li> <li>gromacs.gro - coordinates in Gromacs format (after NTP equalibration)</li> <li>gromacs.top - Gromacs topology </li> </ul> <p> </p>
Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations
<p>This dataset contains the input and output files associated to the work of "Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations"</p> <p> </p> <p> </p>
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Allen Brain Atlas
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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.