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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ftdatacite:10.5281/zenodo.2605372 2023-05-15T17:53:54+02:00 Solvated protein fragments Unke, Oliver Thorsten Meuwly, Markus 2019 https://dx.doi.org/10.5281/zenodo.2605372 https://zenodo.org/record/2605372 unknown Zenodo https://dx.doi.org/10.5281/zenodo.2605371 Open Access Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 info:eu-repo/semantics/openAccess CC-BY proteins amons condensed phase quantum chemistry density functional theory DFT dataset Dataset 2019 ftdatacite https://doi.org/10.5281/zenodo.2605372 https://doi.org/10.5281/zenodo.2605371 2021-11-05T12:55:41Z 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 DataCite Metadata Store (German National Library of Science and Technology) |
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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 |
description |
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 |
publisher |
Zenodo |
publishDate |
2019 |
url |
https://dx.doi.org/10.5281/zenodo.2605372 https://zenodo.org/record/2605372 |
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Orca |
genre_facet |
Orca |
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https://dx.doi.org/10.5281/zenodo.2605371 |
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Open Access Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.5281/zenodo.2605372 https://doi.org/10.5281/zenodo.2605371 |
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