Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Chameleon sequences in neurodegenerative diseases

(2016) Golnaz Bahramali et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks

(2016) Jack Hanson et al.   BIOINFORMATICS

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

Structural database resources for biological macromolecules

(2016) Luciano A. Abriata   BRIEFINGS IN BIOINFORMATICS

Structured States of Disordered Proteins from Genomic Sequences

(2016) Agnes Toth-Petroczy et al.   CELL

Sequence-Based Prediction of Protein–Carbohydrate Binding Sites Using Support Vector Machines

(2016) Ghazaleh Taherzadeh et al.   Journal of Chemical Information and Modeling

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

(2015) Lukas Folkman et al.   BIOINFORMATICS

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins

(2015) Rhys Heffernan et al.   BIOINFORMATICS

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

PPM_One: a static protein structure based chemical shift predictor

(2015) Dawei Li et al.   JOURNAL OF BIOMOLECULAR NMR

The s2D Method: Simultaneous Sequence-Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins

(2015) Pietro Sormanni et al.   JOURNAL OF MOLECULAR BIOLOGY

Advances in Protein Contact Map Prediction Based on Machine Learning

(2015) Jiang Xie et al.   Medicinal Chemistry

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

(2015) Huayan Yang et al.   Nature Protocols

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

(2015) Noor E. Hafsa et al.   NUCLEIC ACIDS RESEARCH

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

(2015) András Micsonai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChSeq: A database of chameleon sequences

(2015) Wenlin Li et al.   PROTEIN SCIENCE

New encouraging developments in contact prediction: Assessment of the CASP11 results

(2015) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis

(2015) Etai Jacob et al.   eLife

Detection oftrans–cisflips and peptide-plane flips in protein structures

(2015) Wouter G. Touw et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

Context-Based Features Enhance Protein Secondary Structure Prediction Accuracy

(2014) Ashraf Yaseen et al.   Journal of Chemical Information and Modeling

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

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Protein Dihedral Angle Prediction Methods

(2014) Harinder Singh et al.   PLoS One

Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility

(2013) C. Mirabello et al.   BIOINFORMATICS

Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation

(2013) Tuo Zhang et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Assessment of template-free modeling in CASP10 and ROLL

(2013) Chin-Hsien Tai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Inactive or moderately active human promoters are enriched for inter-individual epialleles

(2013) Carolina Gemma et al.   GENOME BIOLOGY

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

(2012) Fatemeh Miri Disfani et al.   BIOINFORMATICS

Estimation of Residue-Residue Coevolution using Direct Coupling Analysis Identifies Many Native Contacts Across a Large Number of Domain Families

(2012) Faruck Morcos et al.   BIOPHYSICAL JOURNAL

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction

(2012) S. Saraswathi et al.   JOURNAL OF MOLECULAR MODELING

A Unified Multitask Architecture for Predicting Local Protein Properties

(2012) Yanjun Qi et al.   PLoS One

A novel structural position-specific scoring matrix for the prediction of protein secondary structures

(2011) D. Li et al.   BIOINFORMATICS

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

(2011) Xin Deng et al.   BMC BIOINFORMATICS

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

Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations

(2011) Liang Dai et al.   JOURNAL OF MOLECULAR BIOLOGY

Coarse-grained force field: general folding theory

(2011) Adam Liwo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

CASP9 assessment of free modeling target predictions

(2011) Lisa Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein 8-class secondary structure prediction using conditional neural fields

(2011) Zhiyong Wang et al.   PROTEOMICS

Protein annotation and modelling servers at University College London

(2010) D. W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

Protein fold recognition using sequence-derived predictions

(2010) Daniel Fischer et al.   PROTEIN SCIENCE

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Trends in template/fragment-free protein structure prediction

(2010) Yaoqi Zhou et al.   THEORETICAL CHEMISTRY ACCOUNTS

Lessons from Structural Genomics

(2009) Thomas C. Terwilliger et al.   Annual Review of Biophysics

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

MBA: a literature mining system for extracting biomedical abbreviations

(2009) Yun Xu et al.   BMC BIOINFORMATICS

Mimicking the folding pathway to improve homology-free protein structure prediction

(2009) J. DeBartolo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A force field for virtual atom molecular mechanics of proteins

(2009) A. Korkut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PBOND: Web Server for the Prediction of Proline and Non-Proline cis/trans Isomerization

(2009) Konstantinos P. Exarchos et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A dynamic Bayesian network approach to protein secondary structure prediction

(2008) Xin-Qiu Yao et al.   BMC BIOINFORMATICS

Machine Learning Techniques for Protein Secondary Structure Prediction:An Overview and Evaluation

(2008) Paul Yoo et al.   Current Bioinformatics

Prediction of cis/trans isomerization using feature selection and support vector machines

(2008) Konstantinos P. Exarchos et al.   JOURNAL OF BIOMEDICAL INFORMATICS

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

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

Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks

(2007) Wei Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS