Solvated protein fragments
The solvated protein fragments dataset probes many-body intermolecular interactions between "protein fragments" and water molecules, which are important for the description of many biologically relevant condensed phase systems. It contains structures for all possible "amons" [1]...
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ftzenodo:oai:zenodo.org:2605372 2023-05-15T17:53:55+02:00 Solvated protein fragments Unke, Oliver Thorsten Meuwly, Markus 2019-03-25 https://zenodo.org/record/2605372 https://doi.org/10.5281/zenodo.2605372 unknown arxiv:arXiv:1902.08408 doi:10.5281/zenodo.2605371 https://zenodo.org/record/2605372 https://doi.org/10.5281/zenodo.2605372 oai:zenodo.org:2605372 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode proteins amons condensed phase quantum chemistry density functional theory DFT info:eu-repo/semantics/other dataset 2019 ftzenodo https://doi.org/10.5281/zenodo.260537210.5281/zenodo.2605371 2023-03-11T04:18:25Z The solvated protein fragments dataset probes many-body intermolecular interactions between "protein fragments" and water molecules, which are important for the description of many biologically relevant condensed phase systems. It contains structures for all possible "amons" [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur in different charge states due to (de-)protonation (i.e. carboxylic acids that can be negatively charged or amines that can be positively charged), all possible structures with up to a total charge of +-2e are included. In total, the dataset provides reference energies, forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP level of theory [2-5] using the ORCA 4.0.1 code [6,7]. For more details, see https://arxiv.org/abs/1902.08408. [1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017). [2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010). [3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011). [4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005). [5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998). [6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012). [7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018). Dataset Orca Zenodo |
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proteins amons condensed phase quantum chemistry density functional theory DFT |
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proteins amons condensed phase quantum chemistry density functional theory DFT Unke, Oliver Thorsten Meuwly, Markus Solvated protein fragments |
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proteins amons condensed phase quantum chemistry density functional theory DFT |
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The solvated protein fragments dataset probes many-body intermolecular interactions between "protein fragments" and water molecules, which are important for the description of many biologically relevant condensed phase systems. It contains structures for all possible "amons" [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur in different charge states due to (de-)protonation (i.e. carboxylic acids that can be negatively charged or amines that can be positively charged), all possible structures with up to a total charge of +-2e are included. In total, the dataset provides reference energies, forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP level of theory [2-5] using the ORCA 4.0.1 code [6,7]. For more details, see https://arxiv.org/abs/1902.08408. [1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017). [2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010). [3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011). [4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005). [5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998). [6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012). [7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018). |
format |
Dataset |
author |
Unke, Oliver Thorsten Meuwly, Markus |
author_facet |
Unke, Oliver Thorsten Meuwly, Markus |
author_sort |
Unke, Oliver Thorsten |
title |
Solvated protein fragments |
title_short |
Solvated protein fragments |
title_full |
Solvated protein fragments |
title_fullStr |
Solvated protein fragments |
title_full_unstemmed |
Solvated protein fragments |
title_sort |
solvated protein fragments |
publishDate |
2019 |
url |
https://zenodo.org/record/2605372 https://doi.org/10.5281/zenodo.2605372 |
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arxiv:arXiv:1902.08408 doi:10.5281/zenodo.2605371 https://zenodo.org/record/2605372 https://doi.org/10.5281/zenodo.2605372 oai:zenodo.org:2605372 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.260537210.5281/zenodo.2605371 |
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1766161617169416192 |