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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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In Silico Repurposed Drugs against Monkeypox Virus

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

2022

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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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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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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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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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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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Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange

The Journal of chemical physics, 2009-04, Vol.130 (16), p.164107-164107

Mu, Yuguang

2009

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Hyperfast Water Transport through Biomimetic Nanochannels from Peptide‐Attached (pR)‐pillar[5]arene

Small (Weinheim an der Bergstrasse, Germany), 2019-02, Vol.15 (6), p.e1804678-n/a

2019

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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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Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations

PloS one, 2013-04, Vol.8 (4), p.e60995-e60995

2013

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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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A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids

Journal of chemical theory and computation, 2018-05, Vol.14 (5), p.2733-2742

2018

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Lipid interaction and membrane perturbation of human islet amyloid polypeptide monomer and dimer by molecular dynamics simulations

PloS one, 2012-05, Vol.7 (5), p.e38191-e38191

2012

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Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO)

Physical chemistry chemical physics : PCCP, 2016, Vol.18 (32), p.22081-22088

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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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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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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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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Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: A molecular dynamics study

Nanoscale, 2012-02, Vol.4 (4), p.1154-1159

2012

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

In Silico Repurposed Drugs against Monkeypox Virus

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

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

Effect of A22 on the Conformation of Bacterial Actin MreB

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

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

Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange

Hyperfast Water Transport through Biomimetic Nanochannels from Peptide‐Attached (pR)‐pillar[5]arene

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

Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations

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

A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids

Lipid interaction and membrane perturbation of human islet amyloid polypeptide monomer and dimer by molecular dynamics simulations

Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO)

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

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

Ionic liquid induced inactivation of cellobiohydrolase I from Trichoderma reesei

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

Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: A molecular dynamics study

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