Journal Article

PTPD: predicting therapeutic peptides by deep learning and word2vec

Gao, Rui, Wu, Chuanyan, De Marinis, Yang, Zhang, Yusen

2019

Overview

* Background In the search for therapeutic peptides for disease treatments, many efforts have been made to identify various functional peptides from large numbers of peptide sequence databases. In this paper, we propose an effective computational model that uses deep learning and word2vec to predict therapeutic peptides (PTPD). * Results Representation vectors of all k -mers were obtained through word2vec based on k -mer co-existence information. The original peptide sequences were then divided into k -mers using the windowing method. The peptide sequences were mapped to the input layer by the embedding vector obtained by word2vec. Three types of filters in the convolutional layers, as well as dropout and max-pooling operations, were applied to construct feature maps. These feature maps were concatenated into a fully connected dense layer, and rectified linear units (ReLU) and dropout operations were included to avoid over-fitting of PTPD. The classification probabilities were generated by a sigmoid function. PTPD was then validated using two datasets: an independent anticancer peptide dataset and a virulent protein dataset, on which it achieved accuracies of 96% and 94%, respectively. * Conclusions PTPD identified novel therapeutic peptides efficiently, and it is suitable for application as a useful tool in therapeutic peptide design.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Bioinformatics / Bioinformatics (Computational Biology) / Bioinformatik (Beräkningsbiologi) / Biomedical and Life Sciences / Computational biology / Computational Biology/Bioinformatics / Computer and Information Sciences / Computer Appl. in Life Sciences / Computer applications / Data- och informationsvetenskap (Datateknik) / Datasets / Deep learning / Diseases / Embedding / Feature maps / Health aspects / Identification and classification / Life Sciences / Machine learning / Medical research / Medical treatment / Methodology / Methodology Article / Methods / Microarrays / Natural Sciences / Naturvetenskap / Novel computational methods for the analysis of biological systems / Novels / Peptides / Protein structure prediction / Therapeutic peptide / Word2vec