Abstract
BackgroundPredicting novel drug–target associations is important not only for developing new drugs, but also for furthering biological knowledge by understanding how drugs work and their modes of action. As more data about drugs, targets, and their interactions becomes available, computational approaches have become an indispensible part of drug target association discovery. In this paper we apply random walk with restart (RWR) method to a heterogeneous network of drugs and targets compiled from DrugBank database and investigate the performance of the method under parameter variation and choice of chemical fingerprint methods.ResultsWe show that choice of chemical fingerprint does not affect the performance of the method when the parameters are tuned to optimal values. We use a subset of the ChEMBL15 dataset that contains 2,763 associations between 544 drugs and 467 target proteins to evaluate our method, and we extracted datasets of bioactivity ≤1 and ≤10 μM activity cutoff. For 1 μM bioactivity cutoff, we find that our method can correctly predict nearly 47, 55, 60% of the given drug–target interactions in the test dataset having more than 0, 1, 2 drug target relations for ChEMBL 1 μM dataset in top 50 rank positions. For 10 μM bioactivity cutoff, we find that our method can correctly predict nearly 32.4, 34.8, 35.3% of the given drug–target interactions in the test dataset having more than 0, 1, 2 drug target relations for ChEMBL 1 μM dataset in top 50 rank positions. We further examine the associations between 110 popular top selling drugs in 2012 and 3,519 targets and find the top ten targets for each drug.ConclusionsWe demonstrate the effectiveness and promise of the approach—RWR on heterogeneous networks using chemical features—for identifying novel drug target interactions and investigate the performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0089-z) contains supplementary material, which is available to authorized users.
Highlights
Predicting novel drug–target associations is important for developing new drugs, and for furthering biological knowledge by understanding how drugs work and their modes of action
For binary vectors like chemical fingerprints, it is defined as chemical similarity matrix (Cs)/(A + B − C) where C is the number of bits in common, A is the number of bits in one of the fingerprints, and B is the number of bits in the other fingerprint
Random walk with restart implementation We combined drug–drug, drug–target, and target–target networks into a undirected heterogeneous network
Summary
We show that choice of chemical fingerprint does not affect the performance of the method when the parameters are tuned to optimal values. We use a subset of the ChEMBL15 dataset that contains 2,763 associations between 544 drugs and 467 target proteins to evaluate our method, and we extracted datasets of bioactivity ≤1 and ≤10 μM activity cutoff. For 10 μM bioactivity cutoff, we find that our method can correctly predict nearly 32.4, 34.8, 35.3% of the given drug–target interactions in the test dataset having more than 0, 1, 2 drug target relations for ChEMBL 1 μM dataset in top 50 rank positions. We further examine the associations between 110 popular top selling drugs in 2012 and 3,519 targets and find the top ten targets for each drug
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