EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation

(2017) Konstantinos Kamnitsas et al.   MEDICAL IMAGE ANALYSIS

Application of Artificial Neural Networks for Catalysis: A Review

(2017) Hao Li et al.   Catalysts

Automatic single- and multi-label enzymatic function prediction by machine learning

(2017) Shervine Amidi et al.   PeerJ

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

HCP: A Flexible CNN Framework for Multi-Label Image Classification

(2016) Yunchao Wei et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Computational Approaches for Enzyme Functional Class Prediction: A Review

(2014) Mahesh Sharma et al.   Current Proteomics

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network

(2014) James Lyons et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of enzyme activity with neural network models based on electronic and geometrical features of substrates

(2014) Maciej Szaleniec   Pharmacological Reports

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

A systematic analysis of performance measures for classification tasks

(2009) Marina Sokolova et al.   INFORMATION PROCESSING & MANAGEMENT

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS