142 related articles for article (PubMed ID: 37003731)
1. Path separation of dissipation-corrected targeted molecular dynamics simulations of protein-ligand unbinding.
Wolf S; Post M; Stock G
J Chem Phys; 2023 Mar; 158(12):124106. PubMed ID: 37003731
[TBL] [Abstract][Full Text] [Related]
2. Multisecond ligand dissociation dynamics from atomistic simulations.
Wolf S; Lickert B; Bray S; Stock G
Nat Commun; 2020 Jun; 11(1):2918. PubMed ID: 32522984
[TBL] [Abstract][Full Text] [Related]
3. Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations.
Wolf S; Amaral M; Lowinski M; Vallée F; Musil D; Güldenhaupt J; Dreyer MK; Bomke J; Frech M; Schlitter J; Gerwert K
J Chem Inf Model; 2019 Dec; 59(12):5135-5147. PubMed ID: 31697501
[TBL] [Abstract][Full Text] [Related]
4. Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics.
Zhou S; Weiß RG; Cheng LT; Dzubiella J; McCammon JA; Li B
Proc Natl Acad Sci U S A; 2019 Jul; 116(30):14989-14994. PubMed ID: 31270236
[TBL] [Abstract][Full Text] [Related]
5. Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges.
Wolf S
J Chem Inf Model; 2023 May; 63(10):2902-2910. PubMed ID: 37133392
[TBL] [Abstract][Full Text] [Related]
6. Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics.
Badaoui M; Buigues PJ; Berta D; Mandana GM; Gu H; Földes T; Dickson CJ; Hornak V; Kato M; Molteni C; Parsons S; Rosta E
J Chem Theory Comput; 2022 Apr; 18(4):2543-2555. PubMed ID: 35195418
[TBL] [Abstract][Full Text] [Related]
7. Exploring the Ligand Binding/Unbinding Pathway by Selectively Enhanced Sampling of Ligand in a Protein-Ligand Complex.
Shao Q; Zhu W
J Phys Chem B; 2019 Sep; 123(38):7974-7983. PubMed ID: 31478672
[TBL] [Abstract][Full Text] [Related]
8. Investigation of Rare Protein Conformational Transitions via Dissipation-Corrected Targeted Molecular Dynamics.
Post M; Wolf S; Stock G
J Chem Theory Comput; 2023 Dec; 19(23):8978-8986. PubMed ID: 38011829
[TBL] [Abstract][Full Text] [Related]
9. Enhanced Sampling Simulations of Ligand Unbinding Kinetics Controlled by Protein Conformational Changes.
Zhou Y; Zou R; Kuang G; Långström B; Halldin C; Ågren H; Tu Y
J Chem Inf Model; 2019 Sep; 59(9):3910-3918. PubMed ID: 31454236
[TBL] [Abstract][Full Text] [Related]
10. Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and Compound Design.
Tang Z; Chen SH; Chang CA
J Chem Theory Comput; 2020 Mar; 16(3):1882-1895. PubMed ID: 32031801
[TBL] [Abstract][Full Text] [Related]
11. Predicting Ion Channel Conductance via Dissipation-Corrected Targeted Molecular Dynamics and Langevin Equation Simulations.
Jäger M; Koslowski T; Wolf S
J Chem Theory Comput; 2022 Jan; 18(1):494-502. PubMed ID: 34928150
[TBL] [Abstract][Full Text] [Related]
12. The prediction of protein-ligand unbinding for modern drug discovery.
Zhang Q; Zhao N; Meng X; Yu F; Yao X; Liu H
Expert Opin Drug Discov; 2022 Feb; 17(2):191-205. PubMed ID: 34731059
[TBL] [Abstract][Full Text] [Related]
13. Advances in computational methods for ligand binding kinetics.
Sohraby F; Nunes-Alves A
Trends Biochem Sci; 2023 May; 48(5):437-449. PubMed ID: 36566088
[TBL] [Abstract][Full Text] [Related]
14. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
Votapka LW; Jagger BR; Heyneman AL; Amaro RE
J Phys Chem B; 2017 Apr; 121(15):3597-3606. PubMed ID: 28191969
[TBL] [Abstract][Full Text] [Related]
15. Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations.
Peräkylä M
Eur Biophys J; 2009 Feb; 38(2):185-98. PubMed ID: 18836710
[TBL] [Abstract][Full Text] [Related]
16. Effects of electrostatic interactions on ligand dissociation kinetics.
Erbaş A; de la Cruz MO; Marko JF
Phys Rev E; 2018 Feb; 97(2-1):022405. PubMed ID: 29548245
[TBL] [Abstract][Full Text] [Related]
17. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps.
Tiwary P; Limongelli V; Salvalaglio M; Parrinello M
Proc Natl Acad Sci U S A; 2015 Feb; 112(5):E386-91. PubMed ID: 25605901
[TBL] [Abstract][Full Text] [Related]
18. Learning Protein-Ligand Unbinding Pathways via Single-Parameter Community Detection.
Tänzel V; Jäger M; Wolf S
J Chem Theory Comput; 2024 Jun; 20(12):5058-5067. PubMed ID: 38865714
[TBL] [Abstract][Full Text] [Related]
19. Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods.
Bray S; Tänzel V; Wolf S
J Chem Inf Model; 2022 Oct; 62(19):4591-4604. PubMed ID: 36176219
[TBL] [Abstract][Full Text] [Related]
20. Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations.
Hu G; Xu S; Wang J
Chem Biol Drug Des; 2015 Dec; 86(6):1351-9. PubMed ID: 26032728
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
