Abstract: In this work, we propose a deep learning approach to improve docking-based virtual screening. The introduced deep neural network, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such as atom and amino acid types obtained from protein-ligand complexes. Our approach introduces the use of atom and amino acid embeddings and implements an effective way of creating distributed vector representations of protein-ligand complexes by modeling the compound as a set of atom contexts that is further processed by a convolutional layer. One of the main advantages of the proposed method is that it does not require feature engineering. We evaluate DeepVS on the Directory of Useful Decoys (DUD), using the output of two docking programs: AutodockVina1.1.2 and Dock6.6. Using a…

Link to Full Article: arXiv:1608.04844

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