208 related articles for article (PubMed ID: 31737642)
1. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations.
Wang J; Alekseenko A; Kozakov D; Miao Y
Front Mol Biosci; 2019; 6():112. PubMed ID: 31737642
[TBL] [Abstract][Full Text] [Related]
2. Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding.
Wang J; Miao Y
J Chem Phys; 2020 Oct; 153(15):154109. PubMed ID: 33092378
[TBL] [Abstract][Full Text] [Related]
3. Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations.
Lin WW; Wang YJ; Ko CW; Cheng TL; Wang YT
Polymers (Basel); 2020 Sep; 12(10):. PubMed ID: 32998394
[TBL] [Abstract][Full Text] [Related]
4. Computational modeling of cyclic peptide inhibitor-MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations.
Wang YT; Cheng TL
J Biomol Struct Dyn; 2021 Jul; 39(11):4005-4014. PubMed ID: 32448094
[TBL] [Abstract][Full Text] [Related]
5. Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics.
Wang J; Miao Y
J Chem Theory Comput; 2022 Mar; 18(3):1275-1285. PubMed ID: 35099970
[TBL] [Abstract][Full Text] [Related]
6. Gaussian accelerated molecular dynamics (GaMD): principles and applications.
Wang J; Arantes PR; Bhattarai A; Hsu RV; Pawnikar S; Huang YM; Palermo G; Miao Y
Wiley Interdiscip Rev Comput Mol Sci; 2021; 11(5):. PubMed ID: 34899998
[TBL] [Abstract][Full Text] [Related]
7. ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT.
Porter KA; Xia B; Beglov D; Bohnuud T; Alam N; Schueler-Furman O; Kozakov D
Bioinformatics; 2017 Oct; 33(20):3299-3301. PubMed ID: 28430871
[TBL] [Abstract][Full Text] [Related]
8. Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.
Pawnikar S; Bhattarai A; Wang J; Miao Y
Adv Appl Bioinform Chem; 2022; 15():1-19. PubMed ID: 35023931
[TBL] [Abstract][Full Text] [Related]
9. Gaussian accelerated molecular dynamics for elucidation of drug pathways.
Bhattarai A; Miao Y
Expert Opin Drug Discov; 2018 Nov; 13(11):1055-1065. PubMed ID: 30371112
[TBL] [Abstract][Full Text] [Related]
10. Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.
Miao Y
J Chem Phys; 2018 Aug; 149(7):072308. PubMed ID: 30134710
[TBL] [Abstract][Full Text] [Related]
11. Mechanistic Insights into Peptide Binding and Deactivation of an Adhesion G Protein-Coupled Receptor.
Adediwura VA; Miao Y
Molecules; 2023 Dec; 29(1):. PubMed ID: 38202747
[TBL] [Abstract][Full Text] [Related]
12. Gaussian Accelerated Molecular Dynamics in NAMD.
Pang YT; Miao Y; Wang Y; McCammon JA
J Chem Theory Comput; 2017 Jan; 13(1):9-19. PubMed ID: 28034310
[TBL] [Abstract][Full Text] [Related]
13. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
Schueler-Furman O; Wang C; Baker D
Proteins; 2005 Aug; 60(2):187-94. PubMed ID: 15981249
[TBL] [Abstract][Full Text] [Related]
14. The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations.
Balogh G; Komáromi I; Bereczky Z
J Biomol Struct Dyn; 2020 Oct; 38(16):4718-4732. PubMed ID: 31686597
[TBL] [Abstract][Full Text] [Related]
15. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.
Miao Y; McCammon JA
Annu Rep Comput Chem; 2017; 13():231-278. PubMed ID: 29720925
[TBL] [Abstract][Full Text] [Related]
16. Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.
Gracia Carmona O; Oostenbrink C
J Chem Theory Comput; 2023 Sep; 19(18):6521-6531. PubMed ID: 37649349
[TBL] [Abstract][Full Text] [Related]
17. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.
Miao Y; Feher VA; McCammon JA
J Chem Theory Comput; 2015 Aug; 11(8):3584-3595. PubMed ID: 26300708
[TBL] [Abstract][Full Text] [Related]
18. Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.
Kozakov D; Hall DR; Beglov D; Brenke R; Comeau SR; Shen Y; Li K; Zheng J; Vakili P; Paschalidis ICh; Vajda S
Proteins; 2010 Nov; 78(15):3124-30. PubMed ID: 20818657
[TBL] [Abstract][Full Text] [Related]
19. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration.
Caparotta M; Perez A
J Chem Theory Comput; 2023 Dec; 19(23):8743-8750. PubMed ID: 38039424
[TBL] [Abstract][Full Text] [Related]
20. Gaussian Accelerated Molecular Dynamics in OpenMM.
Copeland MM; Do HN; Votapka L; Joshi K; Wang J; Amaro RE; Miao Y
J Phys Chem B; 2022 Aug; 126(31):5810-5820. PubMed ID: 35895977
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
