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Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Nature communications, 2020-11, Vol.11 (1), p.5713-5713, Article 5713

2020

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ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

Physical chemistry chemical physics : PCCP, 2020-01, Vol.22 (2), p.683-691

2020

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Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3529-3542

2021

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Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants

Journal of chemical information and modeling, 2019-01, Vol.59 (1), p.272-281

2019

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HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models

Journal of chemical information and modeling, 2022-04, Vol.62 (8), p.1830-1839

2022

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DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein-Ligand Interaction Prediction

Molecules (Basel, Switzerland), 2023-06, Vol.28 (12), p.4691

2023

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End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

Chemical reviews, 2019-08, Vol.119 (16), p.9478-9508

2019

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HobPre: accurate prediction of human oral bioavailability for small molecules

Journal of cheminformatics, 2022-01, Vol.14 (1), p.1-1, Article 1

2022

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Protein–Ligand Empirical Interaction Components for Virtual Screening

Journal of chemical information and modeling, 2017-08, Vol.57 (8), p.1793-1806

2017

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An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1

Molecules (Basel, Switzerland), 2024-02, Vol.29 (4), p.881

2024

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Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding

Nanoscale, 2020-04, Vol.12 (13), p.7134-7145

2020

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Effect of Strong Electric Field on the Conformational Integrity of Insulin

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2014-10, Vol.118 (39), p.8942-8952

2014

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MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network

Journal of chemical information and modeling, 2021-07, Vol.61 (7), p.3159-3165

2021

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Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Molecules (Basel, Switzerland), 2023-03, Vol.28 (6), p.2767

2023

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Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method for Full Quantum Mechanical Calculation of Protein Energy

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2013-08, Vol.117 (32), p.7149-7161

2013

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An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity

Nanoscale, 2020-05, Vol.12 (19), p.1737-175

2020

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An Approach to Computing Solvent Reorganization Energy

Journal of chemical theory and computation, 2020-10, Vol.16 (10), p.6513-6519

2020

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DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet

Journal of chemical information and modeling, 2020-03, Vol.60 (3), p.1245-1252

2020

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DeepBSPa Machine Learning Method for Accurate Prediction of Protein–Ligand Docking Structures

Journal of chemical information and modeling, 2021-05, Vol.61 (5), p.2231-2240

2021

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Improving the Scoring of Protein–Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization

Journal of chemical information and modeling, 2013-06, Vol.53 (6), p.1306-1314

2013

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Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds

Journal of the American Chemical Society, 2010-08, Vol.132 (32), p.11159-11164

2010

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Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

Physical chemistry chemical physics : PCCP, 2018, Vol.20 (21), p.14450-14460

2018

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Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Physical chemistry chemical physics : PCCP, 2012-06, Vol.14 (21), p.7837-7845

2012

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Fragment Quantum Mechanical Calculation of Proteins and Its Applications

Accounts of chemical research, 2014-09, Vol.47 (9), p.2748-2757

2014

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Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin−Biotin Binding

Journal of the American Chemical Society, 2010-04, Vol.132 (14), p.5137-5142

2010

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Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis

Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants

HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models

DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein-Ligand Interaction Prediction

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

HobPre: accurate prediction of human oral bioavailability for small molecules

Protein–Ligand Empirical Interaction Components for Virtual Screening

An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding

Effect of Strong Electric Field on the Conformational Integrity of Insulin

MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method for Full Quantum Mechanical Calculation of Protein Energy

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity

An Approach to Computing Solvent Reorganization Energy

DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet

DeepBSPa Machine Learning Method for Accurate Prediction of Protein–Ligand Docking Structures

Improving the Scoring of Protein–Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization

Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Fragment Quantum Mechanical Calculation of Proteins and Its Applications

Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin−Biotin Binding

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