157 related articles for article (PubMed ID: 34739248)
1. Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations.
Sadiq SK; Muñiz Chicharro A; Friedrich P; Wade RC
J Chem Theory Comput; 2021 Dec; 17(12):7912-7929. PubMed ID: 34739248
[TBL] [Abstract][Full Text] [Related]
2. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations.
Chang CE; Trylska J; Tozzini V; McCammon JA
Chem Biol Drug Des; 2007 Jan; 69(1):5-13. PubMed ID: 17313452
[TBL] [Abstract][Full Text] [Related]
3. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.
Deng NJ; Zheng W; Gallicchio E; Levy RM
J Am Chem Soc; 2011 Jun; 133(24):9387-94. PubMed ID: 21561098
[TBL] [Abstract][Full Text] [Related]
4. Assessment of Conformational State Transitions of Class B GPCRs Using Molecular Dynamics.
Liao C; May V; Li J
Methods Mol Biol; 2019; 1947():3-19. PubMed ID: 30969408
[TBL] [Abstract][Full Text] [Related]
5. Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change.
Cai L; Zhou HX
J Chem Phys; 2011 Mar; 134(10):105101. PubMed ID: 21405192
[TBL] [Abstract][Full Text] [Related]
6. Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.
Ren W; Dokainish HM; Shinobu A; Oshima H; Sugita Y
J Phys Chem B; 2021 Mar; 125(11):2898-2909. PubMed ID: 33728914
[TBL] [Abstract][Full Text] [Related]
7. Multiscale computational study of ligand binding pathways: Case of p38 MAP kinase and its inhibitors.
Huang YM
Biophys J; 2021 Sep; 120(18):3881-3892. PubMed ID: 34453922
[TBL] [Abstract][Full Text] [Related]
8. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.
Chang CE; Shen T; Trylska J; Tozzini V; McCammon JA
Biophys J; 2006 Jun; 90(11):3880-5. PubMed ID: 16533835
[TBL] [Abstract][Full Text] [Related]
9. Ligand Binding Pathways and Conformational Transitions of the HIV Protease.
Miao Y; Huang YM; Walker RC; McCammon JA; Chang CA
Biochemistry; 2018 Mar; 57(9):1533-1541. PubMed ID: 29394043
[TBL] [Abstract][Full Text] [Related]
10. Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models.
Plattner N; Noé F
Nat Commun; 2015 Jul; 6():7653. PubMed ID: 26134632
[TBL] [Abstract][Full Text] [Related]
11. Conformational dynamics of a ligand-free adenylate kinase.
Song HD; Zhu F
PLoS One; 2013; 8(7):e68023. PubMed ID: 23861846
[TBL] [Abstract][Full Text] [Related]
12. Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics.
Martin NE; Malik S; Calimet N; Changeux JP; Cecchini M
PLoS Comput Biol; 2017 Oct; 13(10):e1005784. PubMed ID: 29069080
[TBL] [Abstract][Full Text] [Related]
13. CD4-binding obstacles in conformational transitions and allosteric communications of HIV gp120.
Li Y; Guo YC; Zhang XL; Deng L; Sang P; Yang LQ; Liu SQ
Biochim Biophys Acta Biomembr; 2020 Jun; 1862(6):183217. PubMed ID: 32061646
[TBL] [Abstract][Full Text] [Related]
14. Conformational Dynamics in
Muduli S; Karmakar S; Mishra S
J Chem Inf Model; 2024 May; 64(10):4250-4262. PubMed ID: 38701175
[TBL] [Abstract][Full Text] [Related]
15. Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease.
Huang YM; Raymundo MA; Chen W; Chang CA
Biochemistry; 2017 Mar; 56(9):1311-1323. PubMed ID: 28060481
[TBL] [Abstract][Full Text] [Related]
16. Semiclosed Conformations of the Ligand-Binding Domains of NMDA Receptors during Stationary Gating.
Dai J; Zhou HX
Biophys J; 2016 Oct; 111(7):1418-1428. PubMed ID: 27705765
[TBL] [Abstract][Full Text] [Related]
17. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling.
Dokainish HM; Sugita Y
Int J Mol Sci; 2020 Dec; 22(1):. PubMed ID: 33383937
[TBL] [Abstract][Full Text] [Related]
18. Using robotics to fold proteins and dock ligands.
Brutlag D; Apaydin S; Guestrin C; Hsu D; Varma C; Singh A; Latombe JC
Bioinformatics; 2002; 18 Suppl 2():S74. PubMed ID: 12385986
[TBL] [Abstract][Full Text] [Related]
19. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics.
Huang YM; Kang M; Chang CE
J Mol Recognit; 2014 Sep; 27(9):537-48. PubMed ID: 25042708
[TBL] [Abstract][Full Text] [Related]
20. Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations.
Muduli S; Mishra S
Proteins; 2023 Jun; 91(6):781-797. PubMed ID: 36633566
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
