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Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

Journal of chemical information and modeling, 2011-01, Vol.51 (1), p.69-82

2011

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Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models

Journal of cheminformatics, 2021-02, Vol.13 (1), p.12-12, Article 12

2021

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HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

Nucleic acids research, 2019-07, Vol.47 (W1), p.W322-W330

2019

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Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

Physical chemistry chemical physics : PCCP, 2014-08, Vol.16 (31), p.16719-16729

2014

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Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

Journal of computational chemistry, 2011-04, Vol.32 (5), p.866-877

2011

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A unified drug-target interaction prediction framework based on knowledge graph and recommendation system

Nature communications, 2021-11, Vol.12 (1), p.6775-12, Article 6775

2021

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Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

The journal of physical chemistry. B, 2013-07, Vol.117 (28), p.8408-8421

2013

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ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties

Nucleic acids research, 2021-07, Vol.49 (W1), p.W5-W14

2021

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Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking

Physical chemistry chemical physics : PCCP, 2016, Vol.18 (32), p.22129-22139

2016

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Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

Journal of computational chemistry, 2011-12, Vol.32 (16), p.3505-3519

2011

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Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power

Physical chemistry chemical physics : PCCP, 2016, Vol.18 (18), p.12964-12975

2016

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Two-Dimensional MnO2 as a Better Cathode Material for Lithium Ion Batteries

Journal of physical chemistry. C, 2015-12, Vol.119 (52), p.28783-28788

2015

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Janus Structures of Transition Metal Dichalcogenides as the Heterojunction Photocatalysts for Water Splitting

Journal of physical chemistry. C, 2018-02, Vol.122 (5), p.3123-3129

2018

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Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK)

Journal of medicinal chemistry, 2019-12, Vol.62 (24), p.10927-10954

2019

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Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

Journal of proteome research, 2012-05, Vol.11 (5), p.2982-2995

2012

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From machine learning to deep learning: Advances in scoring functions for protein–ligand docking

Wiley interdisciplinary reviews. Computational molecular science, 2020-01, Vol.10 (1), p.e1429-n/a

2020

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Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

Physical chemistry chemical physics : PCCP, 2014-10, Vol.16 (40), p.22035-22045

2014

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Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

Journal of chemical information and modeling, 2012-05, Vol.52 (5), p.1199-1212

2012

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Potential Application of Novel Boron-Doped Graphene Nanoribbon as Oxygen Reduction Reaction Catalyst

Journal of physical chemistry. C, 2016-08, Vol.120 (31), p.17427-17434

2016

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PROTAC-DB 2.0: an updated database of PROTACs

Nucleic acids research, 2023-01, Vol.51 (D1), p.D1367-D1372

2023

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Metformin activates chaperone-mediated autophagy and improves disease pathologies in an Alzheimer disease mouse model

Protein & cell, 2021-10, Vol.12 (10), p.769-787

2021

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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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ARIH1 signaling promotes anti-tumor immunity by targeting PD-L1 for proteasomal degradation

Nature communications, 2021-04, Vol.12 (1), p.2346-14, Article 2346

2021

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Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes

Journal of chemical theory and computation, 2020-06, Vol.16 (6), p.3959-3969

2020

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Molecular Dynamics and Free Energy Studies on the Wild-type and Double Mutant HIV-1 Protease Complexed with Amprenavir and Two Amprenavir-Related Inhibitors: Mechanism for Binding and Drug Resistance

Journal of medicinal chemistry, 2007-03, Vol.50 (6), p.1177-1188

2007

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Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

A unified drug-target interaction prediction framework based on knowledge graph and recommendation system

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power

Two-Dimensional MnO2 as a Better Cathode Material for Lithium Ion Batteries

Janus Structures of Transition Metal Dichalcogenides as the Heterojunction Photocatalysts for Water Splitting

Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK)

Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

From machine learning to deep learning: Advances in scoring functions for protein–ligand docking

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

Potential Application of Novel Boron-Doped Graphene Nanoribbon as Oxygen Reduction Reaction Catalyst

PROTAC-DB 2.0: an updated database of PROTACs

Metformin activates chaperone-mediated autophagy and improves disease pathologies in an Alzheimer disease mouse model

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

ARIH1 signaling promotes anti-tumor immunity by targeting PD-L1 for proteasomal degradation

Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes

Molecular Dynamics and Free Energy Studies on the Wild-type and Double Mutant HIV-1 Protease Complexed with Amprenavir and Two Amprenavir-Related Inhibitors: Mechanism for Binding and Drug Resistance

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