🦠 Model Request: PhaKinPro Incorporation

[sucksido]

Model Name

Pharmacokinetics Profiler (PhaKinPro)

Model Description

Pharmacokinetics Profiler (PhaKinPro) is a recently developed web-based tool that helps predict the pharmacokinetic (PK) properties of drug candidates. In essence, it assists scientists in determining how a drug will behave within the body.
Pharmacokinetics refers to the processes by which a drug is absorbed, distributed, metabolized, and excreted (ADME) . Understanding these processes is critical in drug development, as they can affect a drug's efficacy and safety. For example, a drug that is rapidly metabolized may not be effective in the body, while a drug that is slowly excreted may accumulate to toxic levels.

Slug

PhaKinPro

Tag

Microsomal stability, ADME, Metabolism

Publication

https://pubs.acs.org/doi/10.1021/acs.jmedchem.3c02446

Source Code

https://github.com/molecularmodelinglab/PhaKinPro

License

MIT

[miquelduranfrigola]

Hi @sucksido before approving the model we need to add a bit more information to it. You can see any other working model example to get an idea. Feel free to edit the first comment of the issue for a first attempt!

[sucksido]

Hi @miquelduranfrigola , I have added more details, please let know if that is enough

[miquelduranfrigola]

Hi @sucksido description should be longer in and the tags need to be correct. In this case, this model is not related to malaria, for example. @GemmaTuron @Zainab-ik could you offer assistance/guidelines on writing more complete and correct annotation for the model? Then I will be happy to approve it.

[GemmaTuron]

Hi @sucksido

Please use as guidance what is set in other models. The description must have a minimmum of 250 characters, which you can get by reading the abstract of the paper and summarising it
I do not understand the links to the publication, the source code or the tags. You are pointing to the MAIP model, not PharKinPro. Please modify the links to the correct ones
Also make sure to use the right license

[GemmaTuron]

Hi @sucksido

The information approved for incorporation in the metadata is listed here. For example, ADME and Metabolism would be appropriate tags in this case.
In short, use the tags that are approved, and since python is case sensitive we need to, for example, have the MIT License spelled out as MIT only. For the description, remove the space between paragraphs and make it a single one as otherwise it might cause errors.
Once these are done we can approve the model

[sucksido]

Hi @GemmaTuron , I have updated it

[GemmaTuron]

@sucksido
Please, I listed the appropriate tags for the model - I don't know why you did not add those as well but I have added them.

[GemmaTuron]

/approve

[github-actions]

New Model Repository Created! 🎉

@sucksido ersilia model respository has been successfully created and is available at:

🔗 ersilia-os/eos39dp

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[sucksido]

@GemmaTuron @miquelduranfrigola @JHlozek @DhanshreeA

Findings on PhaKinPro Incorporation: The GitHub repository for PhaKinPro (https://github.com/molecularmodelinglab/PhaKinPro) has seen minimal updates or support in the past two years.
Many functionalities within the repository seem to be dysfunctional.
Significant modifications to the code were necessary to enable proper functionality. For instance, even the basic command python phakinpro.py --help was non-functional until manual adjustments were made to the file PhaKinPro/PhaKinPro/phakinpro.py.
Additionally, the path referencing for the models was incorrect.
The primary issue currently being faced is related to incompatible data types in the pickled model data, resulting in failures to load the data or missing model files.
These issues act as impediments to testing and hinder the generation of the desired CSV outfile.
Attached are both the original and modified versions of phakinpro.py for comparison purposes.
Any assistance in resolving these issues would be greatly appreciated.

[sucksido]

it seems like i cant attach .py files here but I have attached on slack

[sucksido]

Current output: [['SMILES', 'Hepatic Stability', 'Microsomal Half-life Sub-cellular', 'Microsomal Half-life Tissue', 'Renal Clearance', 'BBB Permeability', 'CNS Activity', 'CACO2', 'Plasma Protein Binding', 'Plasma Half-life', 'Microsomal Intrinsic Clearance', 'Oral Bioavailability'], ['CCCCCCCC', '', '', '', '', '', '', '', '', '', '', ''], ['CCCCOCNC', '', '', '', '', '', '', '', '', '', '', ''], ['CCCCNCCCOC', '', '', '', '', '', '', '', '', '', '', '']]

@GemmaTuron does this look

[GemmaTuron]

Hi @sucksido

This is looking good, but I think you might be missing the model checkpoints as all the values are empty? This is the format we want to get from the phakinpro.py function, but make sure the results are actually calculated

[sucksido]

@GemmaTuron I have set up a new Ubuntu env, I also have installed VSCode and Miniconda 3, im bust with model incorporation , busy debugging at the moment, still getting some errors at the moment, currently debugging to make sure we are getting reuslts

[sucksido]

Output:

[['SMILES', 'Hepatic Stability', 'Microsomal Half-life Sub-cellular', 'Microsomal Half-life Tissue', 'Renal Clearance', 'BBB Permeability', 'CNS Activity', 'CACO2', 'Plasma Protein Binding', 'Plasma Half-life', 'Microsomal Intrinsic Clearance', 'Oral Bioavailability'], ['COc1c(/C=N/NC(N)=S)c(CC(C)Cl)c(OC)c2c1OCO2', 0.6733, 0.71, 0.56, None, 0.632, 0.8320000000000001, 0.6679999999999999, 0.596, 0.637, 0.54, 0.5413], ['O=N+c1ccc(N/N=C/c2ccc(N+[O-])s2)cc1', 0.6347, 0.74, 0.52, None, 0.72, 0.828, 0.604, 0.524, 0.5820000000000001, 0.66, 0.58], ['CCCCOc1ccc(N2CC(C(=O)NCCc3ccc(OC)c(OC)c3)CC2=O)cc1', None, 0.53, 0.53, None, 0.604, 0.88, 0.584, 0.516, 0.624, 0.564, 0.54], ['O=C(Nc1cc(Cl)ccc1O)c1ccco1', 0.5533, 0.7, 0.8, None, 0.54, 0.892, 0.688, 0.7559999999999999, None, 0.708, 0.536]]

[sucksido]

Command to run inside: eos39dp/model/framework/ : bash run.sh . ~/test.csv ~/out.csv

[sucksido]

test.csv
Test SMILES

[GemmaTuron]

Hi @sucksido

I've provided feedback on the PR. The automated tests should pass - they provide detailed info on why are they failing, so have a look to amend.
Also while having a look I have noticed that most of the metadata file is empty. You need to fill in all the required fields before pushing the code or the model cannot be appropriately documented and the tests will fail. In GitHub there is a detailed section on what each metadata entry means, and you can also look at other models for inspiration.
thanks

[sucksido]

Hi @GemmaTuron noted thanks, I will fix