Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of …

J Hanson, K Paliwal, T Litfin, Y Yang, Y Zhou - Bioinformatics, 2019 - academic.oup.com
Motivation Sequence-based prediction of one dimensional structural properties of proteins
has been a long-standing subproblem of protein structure prediction. Recently, prediction …

Single‐sequence‐based prediction of protein secondary structures and solvent accessibility by deep whole‐sequence learning

R Heffernan, K Paliwal, J Lyons, J Singh… - Journal of …, 2018 - Wiley Online Library
Predicting protein structure from sequence alone is challenging. Thus, the majority of
methods for protein structure prediction rely on evolutionary information from multiple …

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone …

R Heffernan, Y Yang, K Paliwal, Y Zhou - Bioinformatics, 2017 - academic.oup.com
Motivation The accuracy of predicting protein local and global structural properties such as
secondary structure and solvent accessible surface area has been stagnant for many years …

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 …

SPIDER2: a package to predict secondary structure, accessible surface area, and main-chain torsional angles by deep neural networks

Y Yang, R Heffernan, K Paliwal, J Lyons… - Prediction of protein …, 2017 - Springer
Predicting one-dimensional structure properties has played an important role to improve
prediction of protein three-dimensional structures and functions. The most commonly …

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

R Heffernan, K Paliwal, J Lyons, A Dehzangi… - Scientific reports, 2015 - nature.com
Direct prediction of protein structure from sequence is a challenging problem. An effective
approach is to break it up into independent sub-problems. These sub-problems such as …

[HTML][HTML] Protein secondary structure prediction using deep convolutional neural fields

S Wang, J Peng, J Ma, J Xu - Scientific reports, 2016 - nature.com
Protein secondary structure (SS) prediction is important for studying protein structure and
function. When only the sequence (profile) information is used as input feature, currently the …

Predicting the real‐valued inter‐residue distances for proteins

W Ding, H Gong - Advanced Science, 2020 - Wiley Online Library
Predicting protein structure from the amino acid sequence has been a challenge with
theoretical and practical significance in biophysics. Despite the recent progresses elicited by …

Distill: a suite of web servers for the prediction of one-, two-and three-dimensional structural features of proteins

D Baú, AJM Martin, C Mooney, A Vullo, I Walsh… - BMC …, 2006 - Springer
Abstract Background We describe Distill, a suite of servers for the prediction of protein
structural features: secondary structure; relative solvent accessibility; contact density; …

NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning

MS Klausen, MC Jespersen, H Nielsen… - Proteins: Structure …, 2019 - Wiley Online Library
The ability to predict local structural features of a protein from the primary sequence is of
paramount importance for unraveling its function in absence of experimental structural …