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Predict targets from compound - protein targets associations in ChEMBL22 using one of the following methods

Nearest neighbor search with:

ECfp4 Naive Bayes Machine Learning model produced on the fly with 2000 nearest neighbors from:

Naive Bayes machine learning model with entire dataset using:

Deep Neural Network model with entire dataset using:


Best performing methods are shown in bold. Please refer to manuscript for more details. Shortname is shown for each method.

Recall and Precision statistics considering top 10 predictions

Method Recall (%) Precision (%)
NN(ECfp4) 86 13
NN(Xfp) 81 12
NN(MQN) 76 11
NN(ECfp4) + NB(ECfp4) 76 41
NN(Xfp) + NB(ECfp4) 81 21
NN(MQN) + NB(ECfp4) 78 24
NB(ECfp4) 80 14
DNN(ECfp4) 82 21

How to cite

The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. M. Awale and J.-L. Reymond, 2018, ChemRxiv, doi.org/10.26434/chemrxiv.6895646.v1