280 related articles for article (PubMed ID: 35195418)
1. 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]
2. 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]
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. Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics.
Bianciotto M; Gkeka P; Kokh DB; Wade RC; Minoux H
J Chem Theory Comput; 2021 Oct; 17(10):6522-6535. PubMed ID: 34494849
[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. Baseline Model for Predicting Protein-Ligand Unbinding Kinetics through Machine Learning.
Amangeldiuly N; Karlov D; Fedorov MV
J Chem Inf Model; 2020 Dec; 60(12):5946-5956. PubMed ID: 33183000
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Residence Time Prediction of Type 1 and 2 Kinase Inhibitors from Unbinding Simulations.
Braka A; Garnier N; Bonnet P; Aci-Sèche S
J Chem Inf Model; 2020 Jan; 60(1):342-348. PubMed ID: 31834793
[TBL] [Abstract][Full Text] [Related]
9. 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]
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. 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]
12. Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions.
Lotz SD; Dickson A
J Am Chem Soc; 2018 Jan; 140(2):618-628. PubMed ID: 29303257
[TBL] [Abstract][Full Text] [Related]
13. A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories.
Kokh DB; Doser B; Richter S; Ormersbach F; Cheng X; Wade RC
J Chem Phys; 2020 Sep; 153(12):125102. PubMed ID: 33003755
[TBL] [Abstract][Full Text] [Related]
14. Data-driven classification of ligand unbinding pathways.
Ray D; Parrinello M
Proc Natl Acad Sci U S A; 2024 Mar; 121(10):e2313542121. PubMed ID: 38412121
[TBL] [Abstract][Full Text] [Related]
15. Role of water and steric constraints in the kinetics of cavity-ligand unbinding.
Tiwary P; Mondal J; Morrone JA; Berne BJ
Proc Natl Acad Sci U S A; 2015 Sep; 112(39):12015-9. PubMed ID: 26371312
[TBL] [Abstract][Full Text] [Related]
16. How Robust Is the Ligand Binding Transition State?
Bose S; Lotz SD; Deb I; Shuck M; Lee KSS; Dickson A
J Am Chem Soc; 2023 Nov; 145(46):25318-25331. PubMed ID: 37943667
[TBL] [Abstract][Full Text] [Related]
17. Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations.
Casasnovas R; Limongelli V; Tiwary P; Carloni P; Parrinello M
J Am Chem Soc; 2017 Apr; 139(13):4780-4788. PubMed ID: 28290199
[TBL] [Abstract][Full Text] [Related]
18. Investigating Drug-Target Residence Time in Kinases through Enhanced Sampling Simulations.
Gobbo D; Piretti V; Di Martino RMC; Tripathi SK; Giabbai B; Storici P; Demitri N; Girotto S; Decherchi S; Cavalli A
J Chem Theory Comput; 2019 Aug; 15(8):4646-4659. PubMed ID: 31246463
[TBL] [Abstract][Full Text] [Related]
19. A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors.
Lamim Ribeiro JM; Provasi D; Filizola M
J Chem Phys; 2020 Sep; 153(12):124105. PubMed ID: 33003748
[TBL] [Abstract][Full Text] [Related]
20. Accelerating Rare Dissociative Processes in Biomolecules Using Selectively Scaled MD Simulations.
Deb I; Frank AT
J Chem Theory Comput; 2019 Nov; 15(11):5817-5828. PubMed ID: 31509413
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
