Publications by authors named "Rhys Heffernan"

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Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning.
Rhys Heffernan, Kuldip Paliwal, James Lyons, Jaswinder Singh, Yuedong Yang

J Comput Chem· October 2018

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Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning.
Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip Paliwal, Yuedong Yang

J Chem Inf Model· September 2018

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SPIN2: Predicting sequence profiles from protein structures using deep neural networks.
James O'Connell, Zhixiu Li, Jack Hanson, Rhys Heffernan, James Lyons

Proteins· June 2018

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Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson

Brief Bioinform· May 2018

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SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks.
Yuedong Yang, Rhys Heffernan, Kuldip Paliwal, James Lyons, Abdollah Dehzangi

Methods Mol Biol· January 2018

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Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.
Rhys Heffernan, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou

Bioinformatics· September 2017

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Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.
Rhys Heffernan, Abdollah Dehzangi, James Lyons, Kuldip Paliwal, Alok Sharma

Bioinformatics· March 2016

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Protein fold recognition using HMM-HMM alignment and dynamic programming.
James Lyons, Kuldip K Paliwal, Abdollah Dehzangi, Rhys Heffernan, Tatsuhiko Tsunoda

J Theor Biol· March 2016

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Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models.
James Lyons, Abdollah Dehzangi, Rhys Heffernan, Yuedong Yang, Yaoqi Zhou

IEEE Trans Nanobioscience· October 2015

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Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.
Rhys Heffernan, Kuldip Paliwal, James Lyons, Abdollah Dehzangi, Alok Sharma

Sci Rep· June 2015

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Gram-positive and Gram-negative subcellular localization using rotation forest and physicochemical-based features.
Abdollah Dehzangi, Sohrab Sohrabi, Rhys Heffernan, Alok Sharma, James Lyons

BMC Bioinformatics· May 2015

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Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou׳s general PseAAC.
Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, James Lyons, Kuldip Paliwal

J Theor Biol· January 2015

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Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.
James Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip Paliwal

J Comput Chem· October 2014

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