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27 results for “openff”
modelforge curated dataset: OpenFF PhAlkEthOH Dataset
<h1><strong>Modelforge Curated OpenFF PhAlkEthOH Dataset:<br>- 1000 configuration test set, final energy minimized configuration only<br>- Version: nc_1000_minimal_v1.1</strong></h1> <p>This provides a curated hdf5 file for a subset of the OpenFF PhAlkEthOH dataset designed to be compatible with <a href="https://github.com/choderalab/modelforge">modelforge</a>, an infrastructure to implement and train NNPs. The This dataset contains 1000 unique records for 1000 total configurations. This contains a single configuration corresponding to the final configuration in the optimization trajectory (i.e., the energy minimized configuration).</p> <p>This excludes any configurations where the magnitude of any forces on the atoms are greater than 1 hartree/bohr.</p> <p>When applicable, the units of properties are provided in the datafile, encoded as strings compatible with the <a href="https://github.com/openforcefield/openff-units/">openff-units</a> package. For more information about the structure of the data file, please see the following:</p> <h2><strong>Source Dataset:</strong></h2> <p>PhAlkEthOH: <strong>Ph</strong>enyls, <strong>Alk</strong>anes, <strong>Eth</strong>ers, and alcohols (<strong>OH</strong>) </p> <p>The PhAlkEthOH dataset contains a collection of optimization trajectories of linear and cyclic molecules containing phyl rings, small alkanes, ethers, and alcohols containing only elements carbon, oxygen and hydrogen. For each unique molecule, configurations correspond to snapshots from the optimization trajectory. All QM datapoints retrieved from <a href="https://qcarchive.molssi.org/">The MolSSI qcarchive</a> and were generated using B3LYP-D3BJ/DZVP level of theory, the default theory used for force field development by the Open Force Field Initiative.</p> <h2><strong>Properties Included:</strong></h2> <ul> <li>atomic_numbers </li> <li>positions <ul> <li>"per_atom"</li> <li>"nanometer"</li> </ul> </li> <li>dispersion_correction_gradient <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dispersion_correction_force <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dft_total_gradient <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dft_total_force <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>total_charge <ul> <li>"per_system"</li> <li>"elementary_charge"</li> </ul> </li> <li>dispersion_correction_energy <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>dft_total_energy <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>scf_dipole <ul> <li>"per_system"</li> <li>"elementary_charge * nanometer"</li> </ul> </li> <li>source <ul> <li>"meta_data"</li> </ul> </li> <li>molecular_formula <ul> <li>"meta_data"</li> </ul> </li> <li>canonical_isomeric_explicit_hydrogen_mapped_smiles <ul> <li>"meta_data"</li> </ul> </li> </ul> <h3>Citations:</h3> <p><em>Related manuscripts:</em></p> <ul> <li>Bannan CC, Mobley D. ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns. ChemRxiv. 2019; doi:<a href="https://dx.doi.org/10.26434/chemrxiv.8304578.v1">10.26434/chemrxiv.8304578.v1</a></li> <li>Wang Y, Fass J, Kaminow B, Herr JE, Rufa D, Zhang I, Pulido I, Henry M, Macdonald HE, Takaba K, Chodera JD. End-to-end differentiable construction of molecular mechanics force fields. Chemical Science. 2022;13(41):12016-33. doi:<a href="https://doi.org/10.1039%2Fd2sc02739a" target="_blank" rel="noopener noreferrer">10.1039/d2sc02739a</a></li> </ul> <p><em>Source dataset:</em></p> <ul> <li>Gokey, T,., "OpenFF Sandbox CHO PhAlkEthOH v1.0", 2020, <a href="https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-09-18-OpenFF-Sandbox-CHO-PhAlkEthOH">https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-09-18-OpenFF-Sandbox-CHO-PhAlkEthOH</a></li> </ul>
modelforge curated dataset: SPICE 1 OpenFF
<h1><strong>Modelforge Curated SPICE 1 OpenFF Dataset:</strong><br><strong>- full dataset, limited to [H, C, N, O, F, Cl, S]</strong><br><strong>- Version: full_dataset_HCNOFClS_v2.1<br></strong></h1> <p>This provides a curated hdf5 file for the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with <a href="https://github.com/choderalab/modelforge">modelforge</a>, an infrastructure to implement and train NNPs. This dataset contains 100 unique records for 1000 total configurations, with a maximum of 10 configurations per record.<br>The dataset is limited to the elements that are compatible with ANI2x NNP: [H, C, N, O, F, Cl, S]. This excludes any configurations where the magnitude of any forces <br>on the atoms are greater than 1 hartree/bohr.</p> <p>When applicable, the units of properties are provided in the datafile, encoded as strings compatible with the <a href="https://github.com/openforcefield/openff-units/">openff-units</a> package. </p> <p>This is compatible with modelforge HDF5 schema 2.</p> <p>For more information about the structure of the data file, please see the following:</p> <ul> <li><a href="https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module">https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module</a></li> </ul> <h2><strong>Properties Included:</strong></h2> <ul> <li>atomic_numbers </li> <li>positions <ul> <li>"per_atom"</li> <li>"nanometer"</li> </ul> </li> <li>dft_force <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>mbis_charges <ul> <li>"per_atom"</li> <li>"elementary_charge"</li> </ul> </li> <li>dispersion_correction_force <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dft_total_force <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>total_charge <ul> <li>"per_system"</li> <li>"elementary_charge"</li> </ul> </li> <li>dft_energy <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>scf_dipole <ul> <li>"per_system"</li> <li>"elementary_charge * nanometer"</li> </ul> </li> <li>dispersion_correction_energy <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>dft_total_energy <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>source <ul> <li>"meta_data"</li> </ul> </li> <li>molecular_formula <ul> <li>"meta_data"</li> </ul> </li> <li>canonical_isomeric_explicit_hydrogen_mapped_smiles <ul> <li> "meta_data"<strong><br></strong></li> </ul> </li> </ul> <h2><strong>Source Dataset:</strong></h2> <p>Small-molecule/Protein Interaction Chemical Energies (SPICE).</p> <p>The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. </p> <p>It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1. This is the default theory used for force field development by the <a href="https://openforcefield.org/">Open Force Field Initiative</a>. </p> <div> <p>This includes the following collections from the <a href="https://qcarchive.molssi.org">MolSSI qcarchive</a> (these are also included in the standard SPICE 1 dataset):</p> <ul> <li>"SPICE Solvated Amino Acids Single Points Dataset v1.1",</li> <li>"SPICE Dipeptides Single Points Dataset v1.2",</li> <li>"SPICE DES Monomers Single Points Dataset v1.1",</li> <li>"SPICE DES370K Single Points Dataset v1.0",</li> <li>"SPICE PubChem Set 1 Single Points Dataset v1.2",</li> <li>"SPICE PubChem Set 2 Single Points Dataset v1.2",</li> <li>"SPICE PubChem Set 3 Single Points Dataset v1.2",</li> <li>"SPICE PubChem Set 4 Single Points Dataset v1.2",</li> <li>"SPICE PubChem Set 5 Single Points Dataset v1.2",</li> <li>"SPICE PubChem Set 6 Single Points Dataset v1.2",</li> </ul> </div> <p>This does not include the following collections (which are part of the standard SPICE 1 dataset):</p> <div> <ul> <li>"SPICE Ion Pairs Single Points Dataset v1.1",</li> <li>"SPICE DES370K Single Points Dataset Supplement v1.0",</li> </ul> </div> <h3><strong>Citations:</strong></h3> <p><em>Original SPICE 1 publication:</em></p> <ul> <li>Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). <a href="https://doi.org/10.1038/s41597-022-01882-6">https://doi.org/10.1038/s41597-022-01882-6</a></li> </ul>
OpenFF POPS Simulation with Na+ Counterions (64:64 at 298K)
<p>128 lipid bilayer (64:64) balanced with 128 Na+ ions and hydrated with 4480 SPC/E waters. Equilibrated for 100 ns and simulated for 200 ns at 298K. Full input and output from: https://github.com/PEFrankel/OpenFF_Bilayer.</p><p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange (https://zenodo.org/records/8229243). Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage (Boothroyd et al., 2023 / https://zenodo.org/records/7889050)</p>
OpenFF POPE Simulation (64:64 at 310K)
<p>128 lipid bilayer (64:64) hydrated with 5120 TIP3P waters. Equilibrated for 100 ns and simulated for 200 ns at 310K. Full input and output from: https://github.com/PEFrankel/OpenFF_Bilayer.</p><p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange (https://zenodo.org/records/8229243). Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage (Boothroyd et al., 2023 / https://zenodo.org/records/7889050)</p>
OpenFF POPC Simulation (64:64 at 300K)
<p>128 lipid bilayer (64:64) hydrated with 5000 TIP3P waters. Equilibrated for 100 ns and simulated for 200 ns at 300K. Full input and output from: https://github.com/PEFrankel/OpenFF_Bilayer.</p><p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange (https://zenodo.org/records/8229243). Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage (Boothroyd et al., 2023 / https://zenodo.org/records/7889050)</p>
OpenFF POPC/CHOL 20% Simulation (32/8:32/8 at 298K)
<p>64 lipid bilayer (32:32) with 16 cholesterol molecules (8:8) and hydrated with 4000 SPC/E waters. Equilibrated for 100 ns and simulated for 200 ns at 298K. Full input and output from: https://github.com/PEFrankel/OpenFF_Bilayer.</p><p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange (https://zenodo.org/records/8229243). Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage (Boothroyd et al., 2023 / https://zenodo.org/records/7889050)</p>
OpenFF POPC/CHOL 15% Simulation (55/9:55/9 at 298K)
<p>110 lipid bilayer (64:64) with 18 cholesterol molecules (9:9) and hydrated with 8480 SPC/E waters. Equilibrated for 100 ns and simulated for 200 ns at 298K. Full input and output from: https://github.com/PEFrankel/OpenFF_Bilayer.</p><p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange (https://zenodo.org/records/8229243). Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage (Boothroyd et al., 2023 / https://zenodo.org/records/7889050)</p>
OpenFF POPC (64:64) -- Shortened
<p>128 lipid bilayer (64:64) hydrated with 5120 TIP3P waters. Equilibrated for 100 ns and simulated for 200 ns at 300K</p> <p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange. Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage</p> <p> </p> <p>These files are identical to the previous POPC but shortened to check that NMRLipids Databank works for bilayer thikness, form factor. </p>
OpenFF POPE (64:64)
<p>128 lipid bilayer (64:64) hydrated with 5120 TIP3P waters. Equilibrated for 100 ns and simulated for 200 ns at 300K</p> <p>Partial charges assigned with OpenFF AM1BCC</p> <p>Parameters generated by OpenFF Toolkit (Mobley et al., 2018) + Interchange. Forcefield line: 'openff-2.1.0.offxml' from OpenFF Sage</p> <p> </p> <p>/media/julianne/DATA/Lipids/OpenFFLipid/POPC/</p>
Pure POPE OpenFF Fix Attempt 1
<p>200 ns 64:64 POPE bilayer hydrated with 5000 TIP3P waters.</p>
Pure--No Build--POPE OpenFF Fix Attempt 1
<p>Reused 200 ns 64:64 POPE bilayer hydrated with 5000 TIP3P waters.</p>
POPC JULI OpenFF
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OpenFF 320K HMR
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OpenFF 270K HMR
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OpenFF HMR Whole XTC
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CHARMM and Lipid17 updates for OpenFF Validation
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OpenFF anneal + Lipid21 anneal + CHARMM36 full
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OpenFF POPC Packmol Test
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OpenFF 2.2.0 + NAGL POPC / TRJ Verification
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OpenFF HMR Tests w/ 2.2.0 + NAGL POPC
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