update

model_cards/article.md

@@ -1,68 +1,35 @@
 # Supported molecular properties
 
 
-### ClinTox
-A [ToxSmi model](https://github.com/PaccMann/toxsmi) trained on [ClinTox](https://moleculenet.org/datasets-1) dataset which has two endpoints: Probability of FDA approval and Probability of failure in clinical trials. When using this model, please cite *Born et al. (2023)* (citation below).
+### Instability
+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).
 
-### SIDER
-A [ToxSmi model](https://github.com/PaccMann/toxsmi) trained on the [SIDER](https://moleculenet.org/datasets-1) dataset for 27 different types of side effects of drugs. When using this model, please cite *Born et al. (2023)* (citation below).
+### Aromaticity
+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).
 
-### Tox21
-A [ToxSmi model](https://github.com/PaccMann/toxsmi) trained on the [Tox21](https://tripod.nih.gov/tox/) dataset with 12 different types of environmental toxicities. When using this model, please cite *Born et al. (2023)* (citation below).
+### Isoelectric point
+Computes the isoelectric point of every residue and aggregates.
 
-### SCScore
-Predict the synthetic complexity score (SCScore) as presented in [Coley et al. (*J. Chem. Inf. Model.*; 2018)](https://pubs.acs.org/doi/full/10.1021/acs.jcim.7b00622).
+### Hydrophobicity
+"Computes the hydrophobicity of a protein, relative freq. of **A,C,F,I,L,M & V**.
 
-### SAS
-Estimate the synthetic accessibility score (SAS) as presented in [Ertl et al. (*Journal of Chemoinformatics*; 2009)](https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-1-8).
+### Aliphaticity
+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).
 
-### Lipinski
-Measure whether a molecule confirms to the Lipinski-rule-of-five as presented in [Lipinski et al. (*Advanced Drug Delivery Reviews*; 2001)](https://www.sciencedirect.com/science/article/abs/pii/S0169409X00001290?via%3Dihub).
+### Charge
+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).
 
-### Penalized logP
-Measure the penalized logP (partition coefficient) score as presented in [Gomez-Bombarelli et al. (*ACS Central Science*; 2018)](https://arxiv.org/abs/1610.02415v1). This is the logP minus the number of rings with > 6 atoms minus the SAS.
+### Charge Density
+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).
 
-### QED
-Measure the drug-likeness as presented in [Bickerton et al. (*Nature Chemistry*; 2012)](https://www.nature.com/articles/nchem.1243).
+### Boman index
+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).
 
-### LogP
-Measure the logP (partition coefficient) of a molecule as presented in [Wildman et al. (*J. Chem. Inf. Comput. Sci.*; 1999)](https://pubs.acs.org/doi/full/10.1021/ci990307l).
+### Protein weight
+Compute the molecular weight of a protein with [RDKit](https://www.rdkit.org/docs/GettingStartedInPython.html).
 
-### Bertz
-Calculate the total polar surface area of a molecule as presented in [Ertl et al. (*Journal of Medicinal Chemistry*; 2000)](https://pubs.acs.org/doi/full/10.1021/jm000942e).
+### Length
+Retrieves the number of residues of a protein.
 
-### TPSA
-Calculate the first general index of molecular complexity [Bertz (*Journal of the American Chemical Society*; 1981)](https://pubs.acs.org/doi/pdf/10.1021/ja00402a071).
-
-### Is-Scaffold
-Whether the molecule is identical to its [Murcko scaffold](https://rdkit.org/docs/source/rdkit.Chem.Scaffolds.MurckoScaffold.html).
-
-### Number-Of-X
-Calculated with [RDKit](https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html).
-
-### Molecular Weight
-Calculated with [RDKit](https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html).
-
-
-### ToxSmi citation
-```bib
-@article{born2023chemical,
-  title={Chemical representation learning for toxicity prediction},
-  author={Born, Jannis and Markert, Greta and Janakarajan, Nikita and Kimber, Talia B. and Volkamer, Andrea and Rodriguez Martinez, Maria and Manica, Matteo},
-  journal={Under review at Digital Discovery},
-  year={2023}
-}
-```
-
-
-### Unsupported properties
-The following molecular properties are available via the GT4SD API but not in this UI:
-- [MoleculeOne](https://tdcommons.ai/functions/oracles/#moleculeone) endpoint for retrosynthesis
-- [ASKCOS](https://tdcommons.ai/functions/oracles/#askcos) endpoint for retrosynthesis
-- [TDC-Docking](https://tdcommons.ai/functions/oracles/#docking-scores) endpoint for docking against a user-provided target
-- [TDC-Docking](https://tdcommons.ai/functions/oracles/#docking-scores) endpoint for docking against *3pbl*.
-- [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*.
-- [Tanimoto similarity](https://tdcommons.ai/functions/oracles/#similaritydissimilarity) to a seed molecule.
-
-
-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).
+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).
+The GT4SD web app for molecules can be found [here](https://huggingface.co/spaces/GT4SD/molecular_properties)