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Protein language model-embedded geometric graphs power inter-protein contact prediction

eLife, 2024-04, Vol.12

2024

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MDockPeP: An ab‐initio protein–peptide docking server

Journal of computational chemistry, 2018-10, Vol.39 (28), p.2409-2413

2018

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Preparation and properties of rosin-based cationic waterborne polyurethane dispersion

Colloid and polymer science, 2021-09, Vol.299 (9), p.1489-1498

2021

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HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps

Bioinformatics (Oxford, England), 2017-07, Vol.33 (14), p.2199-2201

2017

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Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Nature methods, 2020-08, Vol.17 (8), p.807-814

2020

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Preparation and pH Detection Performance of Rosin-Based Fluorescent Polyurethane Microspheres

Journal of fluorescence, 2023-07, Vol.33 (4), p.1593-1602

2023

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Genomics and data science: an application within an umbrella

Genome Biology, 2019-05, Vol.20 (1), p.109-109, Article 109

2019

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Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models

Briefings in bioinformatics, 2023-03, Vol.24 (2)

2023

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Protein language model-embedded geometric graphs power inter-protein contact prediction

eLife, 2024-04, Vol.12

2024

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Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2

Briefings in bioinformatics, 2022-07, Vol.23 (4)

2022

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Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function

Briefings in bioinformatics, 2021-11, Vol.22 (6)

2021

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Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark

Journal of chemical information and modeling, 2013-08, Vol.53 (8), p.1905-1914

2013

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Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI)

Proteins, structure, function, and bioinformatics, 2013-12, Vol.81 (12), p.2183-2191

2013

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Predicting peptide binding sites on protein surfaces by clustering chemical interactions

Journal of computational chemistry, 2015-01, Vol.36 (1), p.49-61

2015

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Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

Structure (London), 2016-10, Vol.24 (10), p.1842-1853

2016

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A reproducibility analysis-based statistical framework for residue–residue evolutionary coupling detection

Briefings in bioinformatics, 2022-03, Vol.23 (2)

2022

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A chemical genetic approach demonstrates that MPK3/MPK6 activation and NADPH oxidase‐mediated oxidative burst are two independent signaling events in plant immunity

The Plant journal : for cell and molecular biology, 2014-01, Vol.77 (2), p.222-234

2014

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Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015

Journal of computer-aided molecular design, 2017-08, Vol.31 (8), p.689-699

2017

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Predicting Peptide Binding Sites on Protein Surfaces by Clustering Chemical Interactions

Biophysical journal, 2015-01, Vol.108 (2), p.215a-215a

2015

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Comprehensive functional genomic resource and integrative model for the human brain

Science (American Association for the Advancement of Science), 2018-12, Vol.362 (6420)

2018

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Blind Prediction of Protein-Peptide Complex Structures: A Novel Method and a Web Server

Biophysical journal, 2018-02, Vol.114 (3), p.55a-55a

2018

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The Usage of ACCLUSTER for Peptide Binding Site Prediction

Methods in molecular biology (Clifton, N.J.), 2017, Vol.1561, p.3

2017

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Preparation and properties of rosin-based naphthalene fluorescent polyurethane

Green materials, 2023-05, p.1-9

2023

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Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

Journal of chemical information and modeling, 2016-06, Vol.56 (6), p.1013-1021

2016

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Performance of MDockPP in CAPRI rounds 28‐29 and 31‐35 including the prediction of water‐mediated interactions

Proteins, structure, function, and bioinformatics, 2017-03, Vol.85 (3), p.424-434

2017

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Protein language model-embedded geometric graphs power inter-protein contact prediction

MDockPeP: An ab‐initio protein–peptide docking server

Preparation and properties of rosin-based cationic waterborne polyurethane dispersion

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Preparation and pH Detection Performance of Rosin-Based Fluorescent Polyurethane Microspheres

Genomics and data science: an application within an umbrella

Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models

Protein language model-embedded geometric graphs power inter-protein contact prediction

Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2

Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function

Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI)

Predicting peptide binding sites on protein surfaces by clustering chemical interactions

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction

A reproducibility analysis-based statistical framework for residue–residue evolutionary coupling detection

A chemical genetic approach demonstrates that MPK3/MPK6 activation and NADPH oxidase‐mediated oxidative burst are two independent signaling events in plant immunity

Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015

Predicting Peptide Binding Sites on Protein Surfaces by Clustering Chemical Interactions

Comprehensive functional genomic resource and integrative model for the human brain

Blind Prediction of Protein-Peptide Complex Structures: A Novel Method and a Web Server

The Usage of ACCLUSTER for Peptide Binding Site Prediction

Preparation and properties of rosin-based naphthalene fluorescent polyurethane

Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

Performance of MDockPP in CAPRI rounds 28‐29 and 31‐35 including the prediction of water‐mediated interactions

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