Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training

O Dor, Y Zhou - Proteins: Structure, Function, and …, 2007 - Wiley Online Library
An integrated system of neural networks, called SPINE, is established and optimized for
predicting structural properties of proteins. SPINE is applied to three‐state secondary …

Combining prediction of secondary structure and solvent accessibility in proteins

R Adamczak, A Porollo, J Meller - Proteins: Structure, Function …, 2005 - Wiley Online Library
Owing to the use of evolutionary information and advanced machine learning protocols,
secondary structures of amino acid residues in proteins can be predicted from the primary …

Context-based features enhance protein secondary structure prediction accuracy

A Yaseen, Y Li - Journal of chemical information and modeling, 2014 - ACS Publications
We report a new approach of using statistical context-based scores as encoded features to
train neural networks to achieve secondary structure prediction accuracy improvement. The …

Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties

O Dor, Y Zhou - PROTEINS: Structure, Function, and …, 2007 - Wiley Online Library
Proteins can move freely in three‐dimensional space. As a result, their structural properties,
such as solvent accessible surface area, backbone dihedral angles, and atomic distances …

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

E Faraggi, T Zhang, Y Yang, L Kurgan… - Journal of …, 2012 - Wiley Online Library
Accurate prediction of protein secondary structure is essential for accurate sequence
alignment, three‐dimensional structure modeling, and function prediction. The accuracy of …

Application of multiple sequence alignment profiles to improve protein secondary structure prediction

JA Cuff, GJ Barton - Proteins: Structure, Function, and …, 2000 - Wiley Online Library
The effect of training a neural network secondary structure prediction algorithm with different
types of multiple sequence alignment profiles derived from the same sequences, is shown to …

EVA: large‐scale analysis of secondary structure prediction

B Rost, VA Eyrich - Proteins: Structure, Function, and …, 2001 - Wiley Online Library
EVA is a web‐based server that evaluates automatic structure prediction servers
continuously and objectively. Since June 2000, EVA collected more than 20,000 secondary …

[HTML][HTML] Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

G Pollastri, AJM Martin, C Mooney, A Vullo - BMC bioinformatics, 2007 - Springer
Background Structural properties of proteins such as secondary structure and solvent
accessibility contribute to three-dimensional structure prediction, not only in the ab initio …

Redefining the goals of protein secondary structure prediction

B Rost, C Sander, R Schneider - Journal of molecular biology, 1994 - Elsevier
Secondary structure prediction recently has surpassed the 70% level of average accuracy,
evaluated on the single residue states helix, strand and loop (Q 3). But the ultimate goal is …

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

E Faraggi, B Xue, Y Zhou - Proteins: Structure, Function, and …, 2009 - Wiley Online Library
This article attempts to increase the prediction accuracy of residue solvent accessibility and
real‐value backbone torsion angles of proteins through improved learning. Most methods …