onionnet
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zhenglz
A multiple-layer inter-molecular contact features based deep neural network for protein-ligand binding affinity prediction
Hello, I'm trying to reproduce the pKa predictions for several structures in the [OnionNet_Core_2016](https://github.com/zhenglz/onionnet/blob/master/datasets/output_v2016_predicted.csv) test set, but the values I'm getting differ from those in the paper. Attached is a...
Hi Mr.Zheng, I find the first column in features.csv is lack of a name. `,H_H_0,H_C_1,H_O_2,H_N_3,H_P_4,H_S_5,H_HAX_6,H_DU_7,C_H_8,C_C_9,C_O_10,C_N_11,C_P_12,C_S_13,C_HAX_14,C_DU_15,O_H_16,O_C_17,O_O_18,O_N_19,O_P_20,O_S_21,O_HAX_22,O_DU_23,N_H_24,N_C_25,N_O_26,N_N_27,N_P_28,N_S_29,N_HAX_30,N_DU_31,P_H_32,P_C_33,P_O_34,P_N_35,P_P_36,P_S_37,P_HAX_38,P_DU_39,S_H_40,S_C_41,S_O_42,...` Thus the output prediction csv is also lack of first col-name: `,pKa_predicted` This will bring...
Your env.yaml is `cudatoolkit10 and tensorflow 2.0.0`, which is outdated, and could not be installed by default. And I find there is a sentence 'prefix=/home/zhenglz/...' in the yaml file. What...
OnionNet
Please, why did I encounter this error on the last step to obtain the pKa after obtaining the path? [error.txt](https://github.com/zhenglz/onionnet/files/13185531/error.txt)
About models
When I tried to run predit.py, the h5 file failed to read. I checked the model folder and found that the CNN_final_model_weights.h5 provided was only 1K in size. How can...
Hello, I have followed the installation instructions and I think it went well since I can use the `python generate_features.py -h` but I get this error using the predict.py: ```...
I successfully extracted your features, but an error occurred during my training, errors: No such column pKa_relu in input file 
conda env create -f onionnet_environment.yml should be revised "conda env create -f onionnet_environments.yml"
Greetings, dear colleagues, I am a 5th-year student at Lomonosov Moscow State University. I have **one question about OnionNet**: is it possible to use this neural network to predict "protein-peptide"...
Hi, thanks for this research! I've been playing with the trained model and attempting to reproduce some of the paper's results via the readme instructions. I followed the build, data...
