Supported molecular properties

ClinTox

A ToxSmi model trained on ClinTox dataset which has two endpoints: Probability of FDA approval and Probability of failure in clinical trials. For details see Born et al., (2023; Digital Discovery)

SIDER

A ToxSmi model trained on the SIDER dataset for 27 different types of side effects of drugs. For details see Born et al., (2023; Digital Discovery)

Tox21

A ToxSmi model trained on the Tox21 dataset with 12 different types of environmental toxicities. For details see Born et al., (2023; Digital Discovery)

SCScore

Predict the synthetic complexity score (SCScore) as presented in Coley et al. (J. Chem. Inf. Model.; 2018).

SAS

Estimate the synthetic accessibility score (SAS) as presented in Ertl et al. (Journal of Chemoinformatics; 2009).

Lipinski

Measure whether a molecule confirms to the Lipinski-rule-of-five as presented in Lipinski et al. (Advanced Drug Delivery Reviews; 2001).

Penalized logP

Measure the penalized logP (partition coefficient) score as presented in Gomez-Bombarelli et al. (ACS Central Science; 2018). This is the logP minus the number of rings with > 6 atoms minus the SAS.

QED

Measure the drug-likeness as presented in Bickerton et al. (Nature Chemistry; 2012).

LogP

Measure the logP (partition coefficient) of a molecule as presented in Wildman et al. (J. Chem. Inf. Comput. Sci.; 1999).

Bertz

Calculate the total polar surface area of a molecule as presented in Ertl et al. (Journal of Medicinal Chemistry; 2000).

TPSA

Calculate the first general index of molecular complexity Bertz (Journal of the American Chemical Society; 1981).

Is-Scaffold

Whether the molecule is identical to its Murcko scaffold.

Number-Of-X

Calculated with RDKit.

Molecular Weight

Calculated with RDKit.

ToxSmi citation

@article{born2023chemical,
    author = {Born, Jannis and Markert, Greta and Janakarajan, Nikita and Kimber, Talia B. and Volkamer, Andrea and Martínez, María Rodríguez and Manica, Matteo},
    title = {Chemical representation learning for toxicity prediction},
    journal = {Digital Discovery},
    year = {2023},
    pages = {-},
    publisher = {RSC},
    doi = {10.1039/D2DD00099G},
    url = {http://dx.doi.org/10.1039/D2DD00099G}
}

Unsupported properties

The following molecular properties are available via the GT4SD API but not in this UI:

MoleculeOne endpoint for retrosynthesis
ASKCOS endpoint for retrosynthesis
TDC-Docking endpoint for docking against a user-provided target
TDC-Docking endpoint for docking against 3pbl.
Protein-ligand binding against one of the targets drd2, gsk3b, jnk3, fpscores, cyp3a4_veith, drd2_current, gsk3b_current or jnk3_current.
Tanimoto similarity to a seed molecule.

Moreover, GT4SD also includes properties on other entities such as proteins and crystals. The GT4SD web app for proteins can be found here