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Predicts docking score of small molecules receiving drug molecules based on SMILES and other data

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Literature
Literature
 
 
.gitignore
.gitignore
 
 
Average_Of_Predicted_Docking_Scores_Vs_Observed_Docking_Score_For_BNN_And_1060613_Testing_Observations.png
Average_Of_Predicted_Docking_Scores_Vs_Observed_Docking_Score_For_BNN_And_1060613_Testing_Observations.png
 
 
Conda_Packages.txt
Conda_Packages.txt
 
 
Data_Frame_Of_1060613_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_1060613_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_132577_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_132577_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_132577_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_132577_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_265154_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_265154_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_33145_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_33145_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_33145_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_33145_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_530307_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_530307_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_66289_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_66289_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Data_Frame_Of_66289_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
Data_Frame_Of_66289_Observed_Docking_Scores_And_Averages_And_Standard_Deviations_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.csv
 
 
Diagnose_Inference_Data.py
Diagnose_Inference_Data.py
 
 
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_BNN_With_132577_Training_Or_Testing_Observations.png
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_BNN_With_132577_Training_Or_Testing_Observations.png
 
 
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_BNN_With_33145_Training_Or_Testing_Observations.png
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_BNN_With_33145_Training_Or_Testing_Observations.png
 
 
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_BNN_With_62289_Training_Or_Testing_Observations.png
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_BNN_With_62289_Training_Or_Testing_Observations.png
 
 
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_Bayesian_Model_Using_BART_Model_With_33145_Training_Or_Testing_Observations.png
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_Bayesian_Model_Using_BART_Model_With_33145_Training_Or_Testing_Observations.png
 
 
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_Bayesian_Model_Using_BART_Model_With_66289_Training_Or_Testing_Observations.png
Distributions_Of_Values_Of_Parameter_In_Parameter_Vector_Estimated_As_NUTS_Algorithm_Progresses_For_Bayesian_Model_Using_BART_Model_With_66289_Training_Or_Testing_Observations.png
 
 
Error_Relating_To_Sampling_From_Posterior_Predictive_Probability_Density_Distribution_When_Number_Of_Testing_Observations_Does_Not_Equal_Number_Of_Training_Observations.txt
Error_Relating_To_Sampling_From_Posterior_Predictive_Probability_Density_Distribution_When_Number_Of_Testing_Observations_Does_Not_Equal_Number_Of_Training_Observations.txt
 
 
Excerpt_From_Data_Frame.py
Excerpt_From_Data_Frame.py
 
 
Gains_Curve_For_132577_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
Gains_Curve_For_132577_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
 
 
Gains_Curve_For_132577_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
Gains_Curve_For_132577_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
 
 
Gains_Curve_For_33145_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
Gains_Curve_For_33145_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
 
 
Gains_Curve_For_33145_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
Gains_Curve_For_33145_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
 
 
Gains_Curve_For_66289_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
Gains_Curve_For_66289_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_BNN_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
 
 
Gains_Curve_For_66289_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
Gains_Curve_For_66289_Observed_Docking_Scores_And_Averages_Of_Docking_Scores_Predicted_By_Bayesian_Model_Using_BART_Model_Based_On_Numbers_Of_Occurrences_Of_Substructures.png
 
 
Generate_Feature_Matrices.py
Generate_Feature_Matrices.py
 
 
Instructions_To_Access_Rivanna.pdf
Instructions_To_Access_Rivanna.pdf
 
 
LICENSE
LICENSE
 
 
Naomis_Exploratory_Data_Analysis.ipynb
Naomis_Exploratory_Data_Analysis.ipynb
 
 
Naomis_Multinominal_Posterior_Predictive_Checks.ipynb
Naomis_Multinominal_Posterior_Predictive_Checks.ipynb
 
 
Notes_From_Meetings_With_Naomi_Ohashi_And_Peter_Gedeck.txt
Notes_From_Meetings_With_Naomi_Ohashi_And_Peter_Gedeck.txt
 
 
Notes_From_Meetings_With_Naomi_Ohashi_Regarding_Predicting_Docking_Score_Based_On_SMILES_And_Looked-Up_Fingerprints.txt
Notes_From_Meetings_With_Naomi_Ohashi_Regarding_Predicting_Docking_Score_Based_On_SMILES_And_Looked-Up_Fingerprints.txt
 
 
Notes_From_Meetings_With_Ryan_Weil_Regarding_Predicting_Docking_Score_Based_On_SMILES_And_Looked-Up_Data.txt
Notes_From_Meetings_With_Ryan_Weil_Regarding_Predicting_Docking_Score_Based_On_SMILES_And_Looked-Up_Data.txt
 
 
Plot_Average_Of_Predicted_Docking_Scores_Vs_Observed_Docking_Score.py
Plot_Average_Of_Predicted_Docking_Scores_Vs_Observed_Docking_Score.py
 
 
Plot_Baseline_And_Enrichment_Factor_Vs_Number_Of_Bins.py
Plot_Baseline_And_Enrichment_Factor_Vs_Number_Of_Bins.py
 
 
Plot_Gains_Curve.py
Plot_Gains_Curve.py
 
 
Plot_Probability_Density_Distribution_Of_Docking_Scores.ipynb
Plot_Probability_Density_Distribution_Of_Docking_Scores.ipynb
 
 
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_132577_Training_Or_Testing_Observations_And_BNN.png
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_132577_Training_Or_Testing_Observations_And_BNN.png
 
 
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_33145_Training_Or_Testing_Observations_And_BNN.png
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_33145_Training_Or_Testing_Observations_And_BNN.png
 
 
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_33145_Training_Or_Testing_Observations_And_Bayesian_Model_Using_BART_Model.png
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_33145_Training_Or_Testing_Observations_And_Bayesian_Model_Using_BART_Model.png
 
 
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_66289_Training_Or_Testing_Observations_And_BNN.png
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_66289_Training_Or_Testing_Observations_And_BNN.png
 
 
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_66289_Training_Or_Testing_Observations_And_Bayesian_Model_Using_BART_Model.png
Posterior_Predictive_Check_For_Training_And_Testing_Data_For_66289_Training_Or_Testing_Observations_And_Bayesian_Model_Using_BART_Model.png
 
 
Predict_Response_Values.py
Predict_Response_Values.py
 
 
Presentation.pptx
Presentation.pptx
 
 
Probability_Density_Distribution_Of_Docking_Scores.png
Probability_Density_Distribution_Of_Docking_Scores.png
 
 
Proof_That_PyMC_Model_Can_Have_Different_Numbers_Of_Training_And_Testing_Observations.ipynb
Proof_That_PyMC_Model_Can_Have_Different_Numbers_Of_Training_And_Testing_Observations.ipynb
 
 
Proposal_For_Bayesian_Docking-Score_Predictor.docx
Proposal_For_Bayesian_Docking-Score_Predictor.docx
 
 
README.md
README.md
 
 
Report.docx
Report.docx
 
 
Setup.md
Setup.md
 
 
To-Do_List.txt
To-Do_List.txt
 
 
Toy_Dataset.csv
Toy_Dataset.csv
 
 
Value_Of_Baseline_Or_Enrichment_Factor_Vs_Index_Of_Bin_For_BNN_And_1060613_Testing_Observations.png
Value_Of_Baseline_Or_Enrichment_Factor_Vs_Index_Of_Bin_For_BNN_And_1060613_Testing_Observations.png
 
 
computemeanandvarianceofpredictionsofBARTmodel.py
computemeanandvarianceofpredictionsofBARTmodel.py
 
 

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Bayesian_Docking-Score_Predictor

Predicts docking score of small molecules receiving drug molecules based on SMILES and other data

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Predicts docking score of small molecules receiving drug molecules based on SMILES and other data

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