FreeSolv: A database of experimental and calculated hydration free energies, with input files

By David L. Mobley, J. Guthrie. 2014

502 citations recorded by the source corpus.

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology

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Citations in the corpus

Learning Graph-Level Representation for Drug Discovery (2017, background): “FreeSolv The Free Solvation Database (FreeSolv) provides experimental and calculated hydration free energy of small molecules in water(Mobley and Guthrie 2014).”
Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery (2022, methodology): “…for training and validation are sourced from previously published databases (Syracuse Research Corporation, 1994; Edward W.; Lowe et al., 2011; Mobley and Guthrie, 2014; Wu et al., 2018) and combined with BCL molecule: Unique to remove redundant compounds (see Supplementary Methods for…”
Recent advances and applications of deep learning methods in materials science (2021, unknown): “com/MobleyLab/FreeSolv [86] NOMAD 11mil https://nomad-lab.”
Geometry-enhanced molecular representation learning for property prediction (2021, methodology): “365 • FreeSolv [34] contains the experimental values of free energy of hydration of small 366 molecules in water.”
Enhanced Deep‐Learning Prediction of Molecular Properties via Augmentation of Bond Topology (2018, methodology): “capability of 3DGCN for the prediction of molecular properties, we adopted two datasets— FreeSolv and ESOL—that had widely been used as representative targets for benchmarking the DL models.(34,35) Because the datasets did not provide the 3D structures necessary for the 3D molecular graph in our rep”
Edge Attention-based Multi-Relational Graph Convolutional Networks (2018, background): “Freesolv Freesolv is a database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations [30].”
Graph convolutional networks for computational drug development and discovery (2019, background): “FreeSolv [88] is a database of experimental and calculated hydration free energies for small molecules in water.”
Frustratingly Easy Transferability Estimation (2021, methodology): “We consider four target tasks that predict the molecular ADMET properties, including BBBP [39], BACE [40], Esol [41], FreeSolv [42].”
A fast and high-quality charge model for the next generation general AMBER force field. (2020, methodology): “52 database, 54 and the experimental data of SFEs in organic solvents were obtained from the Minnesota Solvation Database v2012.”
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation (2020, background): “Property prediction of macroscale experimental properties of molecules include quantitative (ESOL [49], FreeSolv [50], PDBbind-F [51]) and categorical (BACE, HIV, ClinTox, Tox21, SIDER, BBBP).”