Dataset Open Access

Solvated protein fragments

Unke, Oliver Thorsten; Meuwly, Markus


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    "description": "<p>The solvated protein fragments dataset probes many-body intermolecular interactions between&nbsp;<br>\n&quot;protein fragments&quot; and water molecules, which are important for the description of many&nbsp;<br>\nbiologically relevant condensed phase systems. It contains structures for all possible&nbsp;<br>\n&quot;amons&quot; [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms&nbsp;<br>\n(C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural<br>\namino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur&nbsp;<br>\nin different charge states due to (de-)protonation (i.e. carboxylic acids that can be&nbsp;<br>\nnegatively charged or amines that can be positively charged), all possible structures with&nbsp;<br>\nup to a total charge of +-2e are included. In total, the dataset provides reference energies,&nbsp;<br>\nforces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP&nbsp;<br>\nlevel of theory [2-5] using the ORCA 4.0.1 code [6,7].&nbsp;</p>\n\n<p>For more details, see https://arxiv.org/abs/1902.08408.</p>\n\n<p>[1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017).<br>\n[2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010).<br>\n[3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011).<br>\n[4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005).<br>\n[5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998).<br>\n[6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012).<br>\n[7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).</p>", 
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    "title": "Solvated protein fragments", 
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    "keywords": [
      "proteins", 
      "amons", 
      "condensed phase", 
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    "publication_date": "2019-03-25", 
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        "affiliation": "University of Basel", 
        "name": "Unke, Oliver Thorsten"
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