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OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein–Ligand Binding Affinity Prediction

ACS omega, 2019-10, Vol.4 (14), p.15956-15965

2019

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Molecular Mechanism of the Inhibition of EGCG on the Alzheimer Aβ1–42 Dimer

The journal of physical chemistry. B, 2013-04, Vol.117 (15), p.3993-4002

2013

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In Silico Repurposed Drugs against Monkeypox Virus

Molecules (Basel, Switzerland), 2022-08, Vol.27 (16), p.5277

2022

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OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells

Frontiers in chemistry, 2021-10, Vol.9, p.753002-753002

2021

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Effect of A22 on the Conformation of Bacterial Actin MreB

International journal of molecular sciences, 2019-03, Vol.20 (6), p.1304

2019

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Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

Scientific reports, 2020-06, Vol.10 (1), p.9685, Article 9685

2020

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Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain

PloS one, 2014-07, Vol.9 (7), p.e101941-e101941

2014

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Liquid–Liquid Phase Separation of Short Histidine- and Tyrosine-Rich Peptides: Sequence Specificity and Molecular Topology

The journal of physical chemistry. B, 2021-07, Vol.125 (25), p.6776-6790

2021

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Electroflocculation of indigo dyeing wastewater from industrial production: Flocs growth and adsorption mechanism

Arabian journal of chemistry, 2023-12, Vol.16 (12), p.105335, Article 105335

2023

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Enantiomeric glycosylated cationic block co-beta-peptides eradicate Staphylococcus aureus biofilms and antibiotic-tolerant persisters

Nature communications, 2019-10, Vol.10 (1), p.4792-14, Article 4792

2019

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Reduction of false positives in structure-based virtual screening when receptor plasticity is considered

Molecules (Basel, Switzerland), 2015-03, Vol.20 (3), p.5152-5164

2015

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Exploring Flexibility of Progesterone Receptor Ligand Binding Domain Using Molecular Dynamics

PloS one, 2016-11, Vol.11 (11), p.e0165824-e0165824

2016

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Amyloid β chaperone - lipocalin-type prostaglandin D synthase acts as a peroxidase in the presence of heme

Biochemical journal, 2020-04, Vol.477 (7), p.1227-1240

2020

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Ionic liquid induced inactivation of cellobiohydrolase I from Trichoderma reesei

Green chemistry : an international journal and green chemistry resource : GC, 2015-01, Vol.17 (3), p.1618-1625

2015

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Energy landscape of a small peptide revealed by dihedral angle principal component analysis

Proteins, structure, function, and bioinformatics, 2005-01, Vol.58 (1), p.45-52

2005

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Cholesterol-stabilized membrane-active nanopores with anticancer activities

Nature communications, 2022-10, Vol.13 (1), p.5985-5985, Article 5985

2022

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Salting Effects on Protein Components in Aqueous NaCl and Urea Solutions: Toward Understanding of Urea-Induced Protein Denaturation

The journal of physical chemistry. B, 2012-02, Vol.116 (4), p.1446-1451

2012

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Structures, Interactions and Activity of the N-Terminal Truncated Variants of Antimicrobial Peptide Thanatin

Antibiotics (Basel), 2024-01, Vol.13 (1), p.74

2024

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SARS-CoV-2 accessory protein 7b forms homotetramers in detergent

Virology journal, 2022-11, Vol.19 (1), p.193-193, Article 193

2022

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The role of pro-inflammatory S100A9 in Alzheimer’s disease amyloid-neuroinflammatory cascade

Acta neuropathologica, 2014-04, Vol.127 (4), p.507-522

2014

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Locking the 150-cavity open: in silico design and verification of influenza neuraminidase inhibitors

PloS one, 2013-08, Vol.8 (8), p.e73344-e73344

2013

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Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein

PloS one, 2009-06, Vol.4 (6), p.e6081-e6081

2009

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Exploring the A22-Bacterial Actin MreB Interaction through Molecular Dynamics Simulations

The journal of physical chemistry. B, 2016-09, Vol.120 (37), p.9867-9874

2016

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The Molecular Basis of Distinct Aggregation Pathways of Islet Amyloid Polypeptide

The Journal of biological chemistry, 2011-02, Vol.286 (8), p.6291-6300

2011

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Plasticity of the 340-Loop in Influenza Neuraminidase Offers New Insight for Antiviral Drug Development

International journal of molecular sciences, 2020-08, Vol.21 (16), p.5655

2020

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OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein–Ligand Binding Affinity Prediction

Molecular Mechanism of the Inhibition of EGCG on the Alzheimer Aβ1–42 Dimer

In Silico Repurposed Drugs against Monkeypox Virus

OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells

Effect of A22 on the Conformation of Bacterial Actin MreB

Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain

Liquid–Liquid Phase Separation of Short Histidine- and Tyrosine-Rich Peptides: Sequence Specificity and Molecular Topology

Electroflocculation of indigo dyeing wastewater from industrial production: Flocs growth and adsorption mechanism

Enantiomeric glycosylated cationic block co-beta-peptides eradicate Staphylococcus aureus biofilms and antibiotic-tolerant persisters

Reduction of false positives in structure-based virtual screening when receptor plasticity is considered

Exploring Flexibility of Progesterone Receptor Ligand Binding Domain Using Molecular Dynamics

Amyloid β chaperone - lipocalin-type prostaglandin D synthase acts as a peroxidase in the presence of heme

Ionic liquid induced inactivation of cellobiohydrolase I from Trichoderma reesei

Energy landscape of a small peptide revealed by dihedral angle principal component analysis

Cholesterol-stabilized membrane-active nanopores with anticancer activities

Salting Effects on Protein Components in Aqueous NaCl and Urea Solutions: Toward Understanding of Urea-Induced Protein Denaturation

Structures, Interactions and Activity of the N-Terminal Truncated Variants of Antimicrobial Peptide Thanatin

SARS-CoV-2 accessory protein 7b forms homotetramers in detergent

The role of pro-inflammatory S100A9 in Alzheimer’s disease amyloid-neuroinflammatory cascade

Locking the 150-cavity open: in silico design and verification of influenza neuraminidase inhibitors

Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein

Exploring the A22-Bacterial Actin MreB Interaction through Molecular Dynamics Simulations

The Molecular Basis of Distinct Aggregation Pathways of Islet Amyloid Polypeptide

Plasticity of the 340-Loop in Influenza Neuraminidase Offers New Insight for Antiviral Drug Development

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