Comments (3)
Hello @LukasChoi, thank you for your interest in our work. You can find the datasets under data folder.
For each dataset:
ligands.txt -> it contains the sequences of drugs (SMILES)
proteins.txt -> it contains the sequences of proteins in the data
affinity.txt -> contains the binding affinity matrix in txt form (drugs x proteins in the same order given in the above text files
Y -> contains the binding affinity matrix in pickle form (drugs x proteins in the same order given in the above text files)
from deepdta.
There are a few questions:
In the /data/davis folder:
- there are two similarities, drug-drug and target-target, what's the criteria of similarity?
- what's the meaning of numbers in the target-target_similarities_WS.txt? I don't think the number means probability.
- what's the standard of affinity? I don't understand the meaning of numbers in drug-atrget_interaction_affinities_Kd__Davis_et_al.2011v1.txt
- there are six test_fold_setting files under "folds" directory, what's the role of these ones? Can you explain the meaning of numbers in the files? For example, [34121, 51548, 12611,...]
In the /data/kiba folder:
5) there two versions of affinity files, kiba_binding_affinity and kiba_binding_affinity_v2, what's the difference?
6) and what's the meaning of 'nan' in the affinity files?
7) there are ligands and proteins files with kiba prefix and without one, kiba_proteins and proteins, what's the difference?
8) what's the role of sim files (kiba_drug_sim and kiba_target_sim)?
In understanding the datasets, your explanation will be very helpful to me.
Thanks in advance.
from deepdta.
Hi @LukasChoi, I made a readme file here and removed some duplicate data. https://github.com/hkmztrk/DeepDTA/blob/master/data/README.md
Could you please refer to this read me and then check out the updated datasets? If there is anything unclear, let me know.
from deepdta.
Related Issues (20)
- model save and load HOT 2
- error message when I ran /DeepDTA/deepdta-toy/run_experiments.py HOT 8
- version of python HOT 1
- The meaning of name for ligands HOT 1
- How can I obtain Pickel file Y for my own ligands and protien datasets ? HOT 1
- Prediction of binding affinity using DeepDTA interpretation HOT 3
- Complete Code HOT 1
- Running "S-W and Pubchem-Sim" case from DeepDTA HOT 3
- the question about the two datasets. HOT 2
- Question about KIBA score HOT 4
- MSE for davis dataset is very high than that is mentioned in the paper HOT 5
- some questions HOT 1
- Could the pre-trained model be made available? HOT 2
- Help with retraining the combined model with a different dataset HOT 2
- new datas HOT 9
- Reimplementation of DeepDTA with Pytorch HOT 2
- I have some questions, can you help me!!! HOT 1
- Help with installation HOT 3
- Question about implementation HOT 4
- During implementation on my own dataset, I got weird results HOT 4
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from deepdta.