title: DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields.
abstract: Intrinsically disordered proteins or protein regions are involved in key biological processes including regulation of transcription, signal transduction, and alternative splicing. Accurately predicting order/disorder regions ab initio from the protein sequence is a prerequisite step for further analysis of functions and mechanisms for these disordered regions. This work presents a learning method, weighted DeepCNF (Deep Convolutional Neural Fields), to improve the accuracy of order/disorder prediction by exploiting the long-range sequential information and the interdependency between adjacent order/disorder labels and by assigning different weights for each label during training and prediction to solve the label imbalance issue. Evaluated by the CASP9 and CASP10 targets, our method obtains 0.855 and 0.898 AUC values, which are higher than the state-of-the-art single ab initio predictors.
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. wangsheng@uchicago.edu.|Toyota Technological Institute at Chicago, Chicago, IL 60637, USA. wangsheng@uchicago.edu.
authors.forename: Sheng
authors.initials: S
authors.lastname: Wang
authors.affiliation: MoE Key Laboratory of Developmental Genetics and Neuropsychiatric Diseases, Bio-X Center, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. wengshunyan@hotmail.com.
authors.forename: Shunyan
authors.initials: S
authors.lastname: Weng
authors.affiliation: Toyota Technological Institute at Chicago, Chicago, IL 60637, USA. majianzhu@gmail.com.
authors.forename: Jianzhu
authors.initials: J
authors.lastname: Ma
authors.affiliation: Toyota Technological Institute at Chicago, Chicago, IL 60637, USA. tqm2004@gmail.com.
authors.forename: Qingming
authors.initials: Q
authors.lastname: Tang
mesh_terms: D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D064267:Intrinsically Disordered Proteins
keywords: conditional neural field; deep convolutional neural network; deep learning; intrinsically disordered proteins; machine learning; prediction of disordered regions