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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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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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PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions

Journal of cheminformatics, 2023-10, Vol.15 (1), p.97-97, Article 97

2023

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ProRefiner: an entropy-based refining strategy for inverse protein folding with global graph attention

Nature communications, 2023-11, Vol.14 (1), p.7434-7434, Article 7434

2023

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MetaRF: attention-based random forest for reaction yield prediction with a few trails

Journal of cheminformatics, 2023-04, Vol.15 (1), p.43-43, Article 43

2023

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Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis

Advanced science, 2022-01, Vol.9 (3), p.e2102435-n/a

2022

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Discovery of Novel Anti‐Resistance AR Antagonists Guided by Funnel Metadynamics Simulation

Advanced science, 2024-05, Vol.11 (19), p.e2309261-n/a

2024

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Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I1/2 NIK Inhibitors

Frontiers in pharmacology, 2019-04, Vol.10, p.345-345

2019

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Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop

Research (Washington), 2024-01, Vol.7, p.0408

2024

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Enabling target-aware molecule generation to follow multi objectives with Pareto MCTS

Communications biology, 2024-09, Vol.7 (1), p.1074-15, Article 1074

2024

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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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Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes

Physical chemistry chemical physics : PCCP, 2019-05, Vol.21 (19), p.1135-1145

2019

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Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions

Physical chemistry chemical physics : PCCP, 2019-09, Vol.21 (35), p.18958-18969

2019

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InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein–Ligand Interaction Predictions

Journal of medicinal chemistry, 2021-12, Vol.64 (24), p.18209-18232

2021

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farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods

Bioinformatics, 2019-05, Vol.35 (10), p.1777-1779

2019

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A novel folding pathway of the villin headpiece subdomain HP35

Physical chemistry chemical physics : PCCP, 2019-08, Vol.21 (33), p.18219-18226

2019

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Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities

Journal of chemical information and modeling, 2020-11, Vol.60 (11), p.5353-5365

2020

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ComDock: A novel approach for protein-protein docking with an efficient fusing strategy

Computers in biology and medicine, 2023-12, Vol.167, p.107660-107660, Article 107660

2023

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VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations

Journal of chemical information and modeling, 2021-06, Vol.61 (6), p.2844-2856

2021

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Rapid screening of multi-point mutations for enzyme thermostability modification by utilizing computational tools

Future generation computer systems, 2024-11, Vol.160, p.724-738

2024

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Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study

Physical chemistry chemical physics : PCCP, 2019-06, Vol.21 (24), p.12931-12947

2019

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Structural view on the role of the TRD loop in regulating DNMT3A activity: a molecular dynamics study

Physical chemistry chemical physics : PCCP, 2022-07, Vol.24 (26), p.15791-1581

2022

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Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?

Briefings in bioinformatics, 2021-09, Vol.22 (5)

2021

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Discovery of a Novel Fusarium Graminearum Mitogen-Activated Protein Kinase (FgGpmk1) Inhibitor for the Treatment of Fusarium Head Blight

Journal of medicinal chemistry, 2021-09, Vol.64 (18), p.13841-13852

2021

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Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power

Briefings in bioinformatics, 2020-01, Vol.21 (1), p.282-297

2020

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

Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes

PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions

ProRefiner: an entropy-based refining strategy for inverse protein folding with global graph attention

MetaRF: attention-based random forest for reaction yield prediction with a few trails

Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis

Discovery of Novel Anti‐Resistance AR Antagonists Guided by Funnel Metadynamics Simulation

Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I1/2 NIK Inhibitors

Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop

Enabling target-aware molecule generation to follow multi objectives with Pareto MCTS

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

Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes

Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions

InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein–Ligand Interaction Predictions

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods

A novel folding pathway of the villin headpiece subdomain HP35

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities

ComDock: A novel approach for protein-protein docking with an efficient fusing strategy

VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations

Rapid screening of multi-point mutations for enzyme thermostability modification by utilizing computational tools

Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study

Structural view on the role of the TRD loop in regulating DNMT3A activity: a molecular dynamics study

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?

Discovery of a Novel Fusarium Graminearum Mitogen-Activated Protein Kinase (FgGpmk1) Inhibitor for the Treatment of Fusarium Head Blight

Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power

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