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The HDOCK server for integrated protein–protein docking

Nature protocols, 2020-05, Vol.15 (5), p.1829-1852

2020

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Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2

Viruses, 2020-04, Vol.12 (4), p.428

2020

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Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

Proteins, structure, function, and bioinformatics, 2017-03, Vol.85 (3), p.497-512

2017

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HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm

Nucleic acids research, 2018-07, Vol.46 (W1), p.W443-W450

2018

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Pushing the accuracy limit of shape complementarity for protein-protein docking

BMC bioinformatics, 2019-12, Vol.20 (Suppl 25), p.696-696, Article 696

2019

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An iterative knowledge-based scoring function for protein-protein recognition

Proteins, structure, function, and bioinformatics, 2008-08, Vol.72 (2), p.557-579

2008

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Advances and challenges in protein-ligand docking

International Journal of Molecular Sciences, 2010-08, Vol.11 (8), p.3016-3034

2010

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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

Proteins, structure, function, and bioinformatics, 2007-02, Vol.66 (2), p.399-421

2007

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Improvement of cryo-EM maps by simultaneous local and non-local deep learning

Nature communications, 2023-06, Vol.14 (1), p.3217-3217, Article 3217

2023

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A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

Nucleic acids research, 2014-04, Vol.42 (7), p.e55-e55

2014

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HDOCK update for modeling protein‐RNA/DNA complex structures

Protein science, 2022-11, Vol.31 (11), p.n/a

2022

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DeepHomo2.0: improved protein–protein contact prediction of homodimers by transformer-enhanced deep learning

Briefings in bioinformatics, 2023-01, Vol.24 (1)

2023

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Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly

Nature communications, 2022-07, Vol.13 (1), p.4066-16, Article 4066

2022

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HCovDock: an efficient docking method for modeling covalent protein–ligand interactions

Briefings in bioinformatics, 2023-01, Vol.24 (1)

2023

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An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials

Journal of computational chemistry, 2006-11, Vol.27 (15), p.1866-1875

2006

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Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes

Nature communications, 2023-08, Vol.14 (1), p.4935-16, Article 4935

2023

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Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46

Proteins, structure, function, and bioinformatics, 2020-08, Vol.88 (8), p.1055-1069

2020

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A nonredundant structure dataset for benchmarking protein-RNA computational docking

Journal of computational chemistry, 2013-02, Vol.34 (4), p.311-318

2013

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Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

Proteins, structure, function, and bioinformatics, 2011-09, Vol.79 (9), p.2648-2661

2011

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Efficient conformational ensemble generation of protein-bound peptides

Journal of cheminformatics, 2017-11, Vol.9 (1), p.59-13, Article 59

2017

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PepBDB: a comprehensive structural database of biological peptide–protein interactions

Bioinformatics, 2019-01, Vol.35 (1), p.175-177

2019

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MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

Proteins, structure, function, and bioinformatics, 2010-11, Vol.78 (15), p.3096-3103

2010

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An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

Journal of computational chemistry, 2006-11, Vol.27 (15), p.1876-1882

2006

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Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

Journal of chemical information and modeling, 2010-02, Vol.50 (2), p.262-273

2010

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Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1

International journal of molecular sciences, 2019-07, Vol.20 (13), p.3325

2019

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The HDOCK server for integrated protein–protein docking

Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2

Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm

Pushing the accuracy limit of shape complementarity for protein-protein docking

An iterative knowledge-based scoring function for protein-protein recognition

Advances and challenges in protein-ligand docking

Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

Improvement of cryo-EM maps by simultaneous local and non-local deep learning

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

HDOCK update for modeling protein‐RNA/DNA complex structures

DeepHomo2.0: improved protein–protein contact prediction of homodimers by transformer-enhanced deep learning

Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly

HCovDock: an efficient docking method for modeling covalent protein–ligand interactions

An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials

Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes

Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46

A nonredundant structure dataset for benchmarking protein-RNA computational docking

Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

Efficient conformational ensemble generation of protein-bound peptides

PepBDB: a comprehensive structural database of biological peptide–protein interactions

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1

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