FAST
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LLNL
Fusion models for Atomic and molecular STructures (FAST)
Hi, It is really not clear to me how this tool can be used to evaluate my own data. For ex, If I want to screen ligands (in mol2 or...
Hi, It seems that the code here can only evaluate the model on PDBBind. How can I use the code to predict the binding affinity of a new complex not...
Hello, Thank you for sharing your project. I cannot understand how to generate the training data but I see you already uploaded sample_data/core_test.hdf. And I don't know how you generated...
Hi, I'm interested to use FAST to do protein-ligand binding prediction, however when I looked at the scripts, they are all referenced to "/p/lscratchh/jones289/data/" which is not found in the...
From FAST/data_util/parse_affinity_data.sh, you use the code " grep -v '#' $path/PDBbind_2016_plain_text_index/index/INDEX_core_data.2016 | cut -f 1 -d ' ' > core.csv" But, I can't find that "INDEX_core_data.2016" from PDBbind_2016_plain_text_index I think...
When I tried the 3dcnn pytorch version, can't reproduce the perasonr mentioned in the paper. The training performance on refine_minus_core set is 0.95(pearsonr), the test performance on core set is...
The code in `data_util` is failing at several places and there are hardcoded file paths all over the place. Any plan to improve the code and make it running without...
Where is the ```model/fusion/main_fusion_pdbbind.py```? Is it the same one to ```model/fusion_tf/main_fusion_pdbbind.py```, or different? Thanks a lot.
The methods in the two files `data_reader.py` and `dnn_general.py` are referenced in the running file , but these two files are not provided in the directory `model/fusion_tf/` https://github.com/LLNL/FAST/blob/b334ab63358eff3ac8edce556bb1c605cd949514/model/fusion_tf/main_fusion_pdbbind.py#L26
