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# Supported molecular properties
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### Is-Scaffold
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Whether the molecule is identical to its [Murcko scaffold](https://rdkit.org/docs/source/rdkit.Chem.Scaffolds.MurckoScaffold.html).
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### Number-Of-X
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Calculated with [RDKit](https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html).
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### Molecular Weight
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Calculated with [RDKit](https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html).
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### ToxSmi citation
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```bib
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@article{born2023chemical,
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title={Chemical representation learning for toxicity prediction},
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author={Born, Jannis and Markert, Greta and Janakarajan, Nikita and Kimber, Talia B. and Volkamer, Andrea and Rodriguez Martinez, Maria and Manica, Matteo},
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journal={Under review at Digital Discovery},
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year={2023}
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}
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```
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### Unsupported properties
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The following molecular properties are available via the GT4SD API but not in this UI:
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- [MoleculeOne](https://tdcommons.ai/functions/oracles/#moleculeone) endpoint for retrosynthesis
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- [ASKCOS](https://tdcommons.ai/functions/oracles/#askcos) endpoint for retrosynthesis
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- [TDC-Docking](https://tdcommons.ai/functions/oracles/#docking-scores) endpoint for docking against a user-provided target
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- [TDC-Docking](https://tdcommons.ai/functions/oracles/#docking-scores) endpoint for docking against *3pbl*.
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- [Protein-ligand binding](https://tdcommons.ai/functions/oracles/#dopamine-receptor-d2-drd2) against one of the targets *drd2*, *gsk3b*, *jnk3*, *fpscores*, *cyp3a4_veith*, *drd2_current*, *gsk3b_current* or *jnk3_current*.
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- [Tanimoto similarity](https://tdcommons.ai/functions/oracles/#similaritydissimilarity) to a seed molecule.
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Moreover, GT4SD also includes properties on other entities such as [proteins](https://gt4sd.github.io/gt4sd-core/api/gt4sd.properties.proteins.html) and [crystals](https://gt4sd.github.io/gt4sd-core/api/gt4sd.properties.crystals.html).
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# Supported molecular properties
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### Instability
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Compute the protein instability as presented in [Guruprasad et al. (*Protein Engineering, Design and Selection*; 1990)](https://academic.oup.com/peds/article-abstract/4/2/155/1491271).
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### Aromaticity
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Compute the protein aromaticity as presented in [Lobry et al. (*Nucleic Acid Research*; 1994)](https://academic.oup.com/nar/article-abstract/22/15/3174/1087817).
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### Isoelectric point
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Computes the isoelectric point of every residue and aggregates.
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### Hydrophobicity
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"Computes the hydrophobicity of a protein, relative freq. of **A,C,F,I,L,M & V**.
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### Aliphaticity
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Compute the aliphatic index of globular proteins as presented in [Ikai (*The Journal of Biochemistry*; 1980)](https://academic.oup.com/jb/article-abstract/88/6/1895/773432).
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### Charge
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Compute the charge of a protein, based on a boolean for the amide (whether the sequences are C-terminally amidated) and a pH value; as presented in [Bjellqvist, (*Electrophoresis*; 1993)](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/elps.11501401163).
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### Charge Density
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Computes the charge density of a protein, based on a boolean for the amide (whether the sequences are C-terminally amidated) and a pH value; as presented in [Bjellqvist, (*Electrophoresis*; 1993)](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/elps.11501401163).
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### Boman index
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Compute the protein aromaticity as presented in [Boman (*Journal of internal medicine*; 2003)](https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2796.2003.01228.x).
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### Protein weight
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Compute the molecular weight of a protein with [RDKit](https://www.rdkit.org/docs/GettingStartedInPython.html).
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### Length
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Retrieves the number of residues of a protein.
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Moreover, GT4SD also includes properties on other entities such as [molecules](https://gt4sd.github.io/gt4sd-core/api/gt4sd.properties.molecules.html) and [crystals](https://gt4sd.github.io/gt4sd-core/api/gt4sd.properties.crystals.html).
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The GT4SD web app for molecules can be found [here](https://huggingface.co/spaces/GT4SD/molecular_properties)
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