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Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK.
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Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.
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Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space.
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Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study.
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Boosted neural networks scoring functions for accurate ligand docking and ranking.
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Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape.
J Chem Inf Model. 2019 Apr 22;59(4):1515-1528. doi: 10.1021/acs.jcim.8b00730. Epub 2019 Mar 28.

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Quantum Mechanics-Based Ranking of Predicted Proteolysis Targeting Chimeras-Mediated Ternary Complexes.
ACS Med Chem Lett. 2025 Feb 6;16(3):420-427. doi: 10.1021/acsmedchemlett.4c00534. eCollection 2025 Mar 13.
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Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach.
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Pinobanksin from peony seed husk: A flavonoid with the potential to inhibit the proliferation of SH-SY5Y.
Food Sci Nutr. 2023 Nov 15;12(2):815-829. doi: 10.1002/fsn3.3786. eCollection 2024 Feb.
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Computer aided drug design in the development of proteolysis targeting chimeras.
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Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.
J Phys Chem A. 2022 Nov 24;126(46):8761-8770. doi: 10.1021/acs.jpca.2c05499. Epub 2022 Nov 8.
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Modeling the Dynamics of Protein-Protein Interfaces, How and Why?
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本文引用的文献

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An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.
Proteins. 2020 Aug;88(8):1029-1036. doi: 10.1002/prot.25869. Epub 2020 Jan 7.
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GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations.
J Chem Inf Model. 2019 Dec 23;59(12):5074-5085. doi: 10.1021/acs.jcim.9b00687. Epub 2019 Dec 12.
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Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu.
Nat Methods. 2020 Jan;17(1):79-85. doi: 10.1038/s41592-019-0637-y. Epub 2019 Nov 25.
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A Structure-Informed Atlas of Human-Virus Interactions.
Cell. 2019 Sep 5;178(6):1526-1541.e16. doi: 10.1016/j.cell.2019.08.005. Epub 2019 Aug 29.
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Evaluation of Predicted Protein-Protein Complexes by Binding Free Energy Simulations.
J Chem Theory Comput. 2019 Mar 12;15(3):2071-2086. doi: 10.1021/acs.jctc.8b01022. Epub 2019 Feb 15.
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Assessment of ab initio models of protein complexes by molecular dynamics.
PLoS Comput Biol. 2018 Jun 4;14(6):e1006182. doi: 10.1371/journal.pcbi.1006182. eCollection 2018 Jun.
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Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach.
J Chem Theory Comput. 2018 Mar 13;14(3):1727-1736. doi: 10.1021/acs.jctc.7b01088. Epub 2018 Feb 9.
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BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery.
J Chem Inf Model. 2018 Feb 26;58(2):219-224. doi: 10.1021/acs.jcim.7b00680. Epub 2018 Jan 31.
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Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Proteins. 2017 Mar;85(3):359-377. doi: 10.1002/prot.25215. Epub 2016 Dec 2.
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dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.
Front Mol Biosci. 2016 Aug 31;3:46. doi: 10.3389/fmolb.2016.00046. eCollection 2016.

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