RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks

(2016) Jianzhao Gao et al.   BIOINFORMATICS

Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area

(2016) Chen Cao et al.   Scientific Reports

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields

(2015) Sheng Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

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

Evaluation of Protein Dihedral Angle Prediction Methods

(2014) Harinder Singh et al.   PLoS One

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

(2012) Jiangning Song et al.   PLoS One

Structural Protein Descriptors in 1-Dimension and their Sequence-Based Predictions

(2011) Lukasz Kurgan et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

(2011) Eshel Faraggi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures

(2010) Petros Kountouris et al.   BMC BIOINFORMATICS

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

(2009) Petros Kountouris et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction

(2009) Eshel Faraggi et al.   STRUCTURE

SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

(2008) Wei Zhang et al.   PLoS One

ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction

(2008) Sitao Wu et al.   PLoS One

Fragment-HMM: A new approach to protein structure prediction

(2008) Shuai Cheng Li et al.   PROTEIN SCIENCE

Real-value prediction of backbone torsion angles

(2008) Bin Xue et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network

(2008) Eshel Faraggi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

TALI: LOCAL ALIGNMENT OF PROTEIN STRUCTURES USING BACKBONE TORSION ANGLES

(2008) XIJIANG MIAO et al.   Journal of Bioinformatics and Computational Biology