Prediction of protein function using a deep convolutional neural network ensemble

• Published in: PeerJ. Computer science 2017-07, Vol.3, p.e124-17, Article e124
• Main Author: Zacharaki, Evangelia I
• Format: Article
• Language: English
• Subjects: Amino acids; Analysis; Annotations; Applied research; Artificial intelligence; Artificial neural networks; Bioinformatics; Classification; Computer Science; Convolutional neural networks; Deep learning; Enzyme classification; Enzymes; Exploitation; Feature extraction; Feature maps; Function predition; Homology; International conferences; K-nearest neighbors algorithm; Machine Learning; Methods; Molecular biology; Pharmacology; Protein structure prediction; Proteins; Structure representation; Support vector machines; Target recognition; Three dimensional models; Wavelet transforms
• ISSN: 2376-5992; 2376-5992
• DOI: 10.7717/peerj-cs.124

The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function prediction. In this work, novel shape features are extracted representing protein structure in the form of local (per amino acid) distribution of angles and amino acid distances, respectively. Each of the multi-channel feature maps is introduced into a deep convolutional neural network (CNN) for function prediction and the outputs are fused through support vector machines or a correlation-based k-nearest neighbor classifier. Two different architectures are investigated employing either one CNN per multi-channel feature set, or one CNN per image channel. Cross validation experiments on single-functional enzymes (n=44,661) from the PDB database achieved 90.1% correct classification, demonstrating an improvement over previous results on the same dataset when sequence similarity was not considered. The automatic prediction of protein function can provide quick annotations on extensive datasets opening the path for relevant applications, such as pharmacological target identification. The proposed method shows promise for structure-based protein function prediction, but sufficient data may not yet be available to properly assess the method's performance on non-homologous proteins and thus reduce the confounding factor of evolutionary relationships.