Target Binding and Sequence Prediction With LSTMs

Abstract

Deep recurrent neural networks (DRNNs) have recently demonstrated strong performance in sequential data analysis, such as natural language processing. These capabilities make them a promising tool for inferential analysis of sequentially structured bioinformatics data as well. Here, we assessed the ability of Long Short-Term Memory (LSTM) networks, a class of DRNNs, to predict properties of proteins based on their primary structures. The proposed architecture is trained and tested on two different datasets to predict whether a given sequence falls into a certain class or not. The first dataset, directly imported from Uniprot, was used to train the network on whether a given protein contained or did not contain a conserved sequence (homeodomain), and the second dataset, derived by literature mining, was used to train a network on whether a given protein binds or doesn't bind to Artemisinin, a drug typically used to treat malaria. In each case, the model was able to differentiate between the two different classes of sequences it was given with high accuracy, illustrating successful learning and generalization. Upon completion of training, an ROC curve was created using the homeodomain and artemisinin validation datasets. The AUC of these datasets was 0.80 and 0.87 respectively, further indicating the models' effectiveness. Furthermore, using these trained models, it was possible to derive a protocol for sequence detection of homeodomain and binding motif, which are well-documented in literature, and a known Artemisinin binding site, respectively [1][2][3]. Along with these contributions, we developed a python API to directly connect to Uniprot data sourcing, train deep neural networks on this primary sequence data using TensorFlow, and uniquely visualize the results of this analysis. Such an approach has the potential to drastically increase accuracy and reduce computational time and, current major limitations in informatics, from inquiry to discovery in protein function research.