Dataset
solvated_protein_fragments_JCTC_2019
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| Name | solvated_protein_fragments_JCTC_2019 |
|---|---|
| Extended ID | solvated_protein_fragments_JCTC_2019__Unke-Meuwly__DS_ctjgc03xdauc_0 |
| Description | The solvated protein fragments dataset was generated as a partner benchmark dataset, along with SN2, for measuring the performance of machine learning models, in particular PhysNet, at describing chemical reactions, long-range interactions, and condensed phase systems. The dataset contains structures for all possible "amons" (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 2,731,180 structures calculated at the revPBE-D3(BJ)/def2-TZVP level of theory using ORCA 4.0.1. |
| Authors |
Oliver T. Unke Markus Meuwly |
| DOI |
10.60732/c4731f07
https://commons.datacite.org/doi.org/10.60732/c4731f07 https://doi.datacite.org/dois/10.60732%2Fc4731f07 https://doi.org/10.60732/c4731f07 Cite as: Unke, O. T., and Meuwly, M. "solvated protein fragments JCTC 2019." ColabFit, 2023. https://doi.org/10.60732/c4731f07. For other citation formats, see the DataCite Fabrica page for this dataset. |
| Calculated Property Types |
atomic_forces cauchy_stress energy |
| Elements |
C (19.27%) H (63.04%) N (4.88%) O (11.69%) S (1.13%) |
| Number of Configurations | 2,731,180 |
| Number of Atoms | 58,395,272 |
| Links |
https://doi.org/10.5281/zenodo.2605372 https://doi.org/10.1021/acs.jctc.9b00181 |
| Configuration Sets by Name | (None) |
| Configuration Sets by ID | (None) |
| Calculated Properties | |
| ColabFit ID | DS_ctjgc03xdauc_0 |
| Files | colabfitspec.json |
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