219 related articles for article (PubMed ID: 36346951)
1. Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.
Ruzmetov T; Montes R; Sun J; Chen SH; Tang Z; Chang CA
J Phys Chem A; 2022 Nov; 126(46):8761-8770. PubMed ID: 36346951
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach.
Ahn SH; Jagger BR; Amaro RE
J Chem Inf Model; 2020 Nov; 60(11):5340-5352. PubMed ID: 32315175
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. The free energy landscape of small molecule unbinding.
Huang D; Caflisch A
PLoS Comput Biol; 2011 Feb; 7(2):e1002002. PubMed ID: 21390201
[TBL] [Abstract][Full Text] [Related]
8. Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein.
Tripathi S; Nair NN
J Chem Inf Model; 2023 Aug; 63(16):5182-5191. PubMed ID: 37540828
[TBL] [Abstract][Full Text] [Related]
9. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.
Wang J; Shao Q; Xu Z; Liu Y; Yang Z; Cossins BP; Jiang H; Chen K; Shi J; Zhu W
J Phys Chem B; 2014 Jan; 118(1):134-43. PubMed ID: 24350625
[TBL] [Abstract][Full Text] [Related]
10. Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape.
Re S; Oshima H; Kasahara K; Kamiya M; Sugita Y
Proc Natl Acad Sci U S A; 2019 Sep; 116(37):18404-18409. PubMed ID: 31451651
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.
Ojha AA; Votapka LW; Amaro RE
Chem Sci; 2023 Nov; 14(45):13159-13175. PubMed ID: 38023523
[TBL] [Abstract][Full Text] [Related]
13. Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.
Chiu SH; Xie L
J Chem Inf Model; 2016 Jun; 56(6):1164-74. PubMed ID: 27159844
[TBL] [Abstract][Full Text] [Related]
14. Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison.
Sun J; Raymundo MAV; Chang CA
Life (Basel); 2022 Jan; 12(1):. PubMed ID: 35054509
[TBL] [Abstract][Full Text] [Related]
15. Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.
Tang Z; Chang CA
J Chem Theory Comput; 2018 Jan; 14(1):303-318. PubMed ID: 29149564
[TBL] [Abstract][Full Text] [Related]
16. Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?
You W; Tang Z; Chang CA
J Chem Theory Comput; 2019 Apr; 15(4):2433-2443. PubMed ID: 30811931
[TBL] [Abstract][Full Text] [Related]
17. New approaches for computing ligand-receptor binding kinetics.
Bruce NJ; Ganotra GK; Kokh DB; Sadiq SK; Wade RC
Curr Opin Struct Biol; 2018 Apr; 49():1-10. PubMed ID: 29132080
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. 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]
20. Mapping the Ligand Binding Landscape.
Dickson A
Biophys J; 2018 Nov; 115(9):1707-1719. PubMed ID: 30327139
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]