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4 results for “Protein solvation”
DATASET: Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona
<p>This dataset contains the DLS, CD, fluorescence, ITC, TEM, and ANS raw data used for the manuscript.</p>
Solvated protein fragments
<p>The solvated protein fragments dataset probes many-body intermolecular interactions between <br> "protein fragments" and water molecules, which are important for the description of many <br> biologically relevant condensed phase systems. It contains structures for all possible <br> "amons" [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms <br> (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural<br> amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur <br> in different charge states due to (de-)protonation (i.e. carboxylic acids that can be <br> negatively charged or amines that can be positively charged), all possible structures with <br> up to a total charge of +-2e are included. In total, the dataset provides reference energies, <br> forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP <br> level of theory [2-5] using the ORCA 4.0.1 code [6,7]. </p> <p>For more details, see https://arxiv.org/abs/1902.08408.</p> <p>[1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017).<br> [2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010).<br> [3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011).<br> [4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005).<br> [5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998).<br> [6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012).<br> [7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).</p>
Solvated Protein Fragments (QCArchive View Formatted)
<p>Data curated by the QCArchive team, originally sourced from quantum-machine.org.</p> <p>Water-solvated protein fragments with up to 8 heavy atoms. Configurations are generated from MD, evaluated at the revPBE-D3(BJ)/def2-TZVP level of theory. Also included are fragment dimers and clusters of up to 40 water molecules.</p> <p>For more information, see http://qcarchive.molssi.org/apps/ml_datasets/.</p>
DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein–Ligand Binding Affinity Prediction
<p><strong>structures.zip:</strong> including the coordinates of all optimized proteinligand complex structure obtained by DOX_BDW calculation. (compressed PDB file). These pdb files could also be used as input for the binding energy calculation,as illustrated in SI section 8. </p> <p><strong>mdinput.zip:</strong> Including the input files,parameter files, topology files needed to run MD simulation for water mapping, as illustrated in SI section 8. Note that all of the parameter files and topology files would be automatically generated using the RUNMD program we uploaded with the example file. </p> <p><strong>example.zip:</strong> The programs and input files needed to run an example, as illustrated in SI section 9. And all the output files except MD trajectories are in there,too.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.