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RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

Nature communications, 2019-11, Vol.10 (1), p.5407-13, Article 5407

2019

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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

Bioinformatics (Oxford, England), 2017-09, Vol.33 (18), p.2842-2849

2017

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

Bioinformatics (Oxford, England), 2017-03, Vol.33 (5), p.685-692

2017

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Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

Bioinformatics, 2011-08, Vol.27 (15), p.2076-2082

2011

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

Briefings in bioinformatics, 2018-05, Vol.19 (3), p.482-494

2018

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Astronomical forcing of a Middle Permian chert sequence in Chaohu, South China

Earth and planetary science letters, 2015-07, Vol.422, p.206-221

2015

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Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

Nature communications, 2021-05, Vol.12 (1), p.2777-2777, Article 2777

2021

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

Scientific reports, 2015-06, Vol.5 (1), p.11476-11476, Article 11476

2015

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Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

Nature communications, 2017-03, Vol.8 (1), p.14902-14902, Article 14902

2017

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

Journal of computational chemistry, 2018-10, Vol.39 (26), p.2210-2216

2018

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Recent advances in glycoinformatic platforms for glycomics and glycoproteomics

Current opinion in structural biology, 2020-06, Vol.62, p.56-69

2020

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Structural insights into the histone H1-nucleosome complex

Proceedings of the National Academy of Sciences - PNAS, 2013-11, Vol.110 (48), p.19390-19395

2013

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SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

Genomics, proteomics & bioinformatics, 2019-12, Vol.17 (6), p.645-656

2019

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Elemental and Sr-Nd-Pb-Hf isotope signatures of Early Cretaceous magmatic rocks in the Wulian area, eastern Shandong; implications for crust-mantle interaction at the edge of the Sulu collisional orogenic belt

Lithosphere, 2022-01, Vol.2022 (1)

2022

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SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1484, p.55

2017

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SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network

PLoS computational biology, 2023-12, Vol.19 (12), p.e1011330-e1011330

2023

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Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

Protein science, 2002-11, Vol.11 (11), p.2714-2726

2002

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SPIN2: Predicting sequence profiles from protein structures using deep neural networks

Proteins, structure, function, and bioinformatics, 2018-06, Vol.86 (6), p.629-633

2018

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Sequence-based prediction of protein-peptide binding sites using support vector machine

Journal of computational chemistry, 2016-05, Vol.37 (13), p.1223-1229

2016

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High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5′-OH-end linker and unique 3′-P-end fragments from hydroxyl radical cleavage

RNA biology, 2022-12, Vol.19 (1), p.1179-1189

2022

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

Proteins, structure, function, and bioinformatics, 2007-03, Vol.66 (4), p.838-845

2007

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Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment

Scientific reports, 2022-05, Vol.12 (1), p.7607-7607, Article 7607

2022

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Geochemistry of the Laiyang Group from outcrops and Lingke-1 core on Lingshan Island, Shandong Province, eastern China; implications for provenance, tectonic setting and palaeoenvironment

Geological magazine, 2022-01, Vol.159 (1), p.37-54

2022

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

Bioinformatics, 2016-03, Vol.32 (6), p.843-849

2016

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Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures

BMC bioinformatics, 2018-02, Vol.19 (1), p.29-8, Article 29

2018

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RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

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

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

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

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

Astronomical forcing of a Middle Permian chert sequence in Chaohu, South China

Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

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

Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

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

Recent advances in glycoinformatic platforms for glycomics and glycoproteomics

Structural insights into the histone H1-nucleosome complex

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

Elemental and Sr-Nd-Pb-Hf isotope signatures of Early Cretaceous magmatic rocks in the Wulian area, eastern Shandong; implications for crust-mantle interaction at the edge of the Sulu collisional orogenic belt

SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks

SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network

Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

SPIN2: Predicting sequence profiles from protein structures using deep neural networks

Sequence-based prediction of protein-peptide binding sites using support vector machine

High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5′-OH-end linker and unique 3′-P-end fragments from hydroxyl radical cleavage

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

Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment

Geochemistry of the Laiyang Group from outcrops and Lingke-1 core on Lingshan Island, Shandong Province, eastern China; implications for provenance, tectonic setting and palaeoenvironment

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

Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures

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