Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
نویسندگان
چکیده
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.
منابع مشابه
Protein Secondary Structure Prediction Using Deep Multi-scale Convolutional Neural Networks and Next-Step Conditioning
Recently developed deep learning techniques have significantly improved the accuracy of various speech and image recognition systems. In this paper we adapt some of these techniques for protein secondary structure prediction. We first train a series of deep neural networks to predict eight-class secondary structure labels given a protein’s amino acid sequence information and find that using rec...
متن کاملProtein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks
Protein secondary structure prediction is an important problem in bioinformatics. Inspired by the recent successes of deep neural networks, in this paper, we propose an end-to-end deep network that predicts protein secondary structures from integrated local and global contextual features. Our deep architecture leverages convolutional neural networks with different kernel sizes to extract multis...
متن کاملDeep Learning Approach for Secondary Structure Protein Prediction based on First Level Features Extraction using a Latent CNN Structure
In Bioinformatics, Protein Secondary Structure Prediction (PSSP) has been considered as one of the main challenging tasks in this field. Today, secondary structure protein prediction approaches have been categorized into three groups (Neighbor-based, model-based, and meta predicator-based model). The main purpose of the model-based approaches is to detect the protein sequence-structure by utili...
متن کاملNext-Step Conditioned Deep Convolutional Neural Networks Improve Protein Secondary Structure Prediction
Motivation: Recently developed deep learning techniques have significantly improved the accuracy of various speech and image recognition systems. In this paper we show how to adapt some of these techniques to create a novel chained convolutional architecture with next-step conditioning for improving performance on protein sequence prediction problems. We explore its value by demonstrating its a...
متن کاملMUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-Based Protein Structure Prediction
Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer perceptron. Taking inspiration from the image classification domain we propose a deep convolutional neural network architecture, MUST-CNN, to pr...
متن کامل