243 related articles for article (PubMed ID: 26505480)
1. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.
Votapka LW; Amaro RE
PLoS Comput Biol; 2015 Oct; 11(10):e1004381. PubMed ID: 26505480
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.
Jagger BR; Lee CT; Amaro RE
J Phys Chem Lett; 2018 Sep; 9(17):4941-4948. PubMed ID: 30070844
[TBL] [Abstract][Full Text] [Related]
5. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
Foffi G; Pastore A; Piazza F; Temussi PA
Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
[TBL] [Abstract][Full Text] [Related]
6. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.
Votapka LW; Stokely AM; Ojha AA; Amaro RE
J Chem Inf Model; 2022 Jul; 62(13):3253-3262. PubMed ID: 35759413
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics.
Bucci A; Yu TQ; Vanden-Eijnden E; Abrams CF
J Chem Theory Comput; 2016 Jun; 12(6):2964-72. PubMed ID: 27168219
[TBL] [Abstract][Full Text] [Related]
9. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach.
Jagger BR; Ojha AA; Amaro RE
J Chem Theory Comput; 2020 Aug; 16(8):5348-5357. PubMed ID: 32579371
[TBL] [Abstract][Full Text] [Related]
10. Role of anisotropy for protein-protein encounter.
Schluttig J; Korn CB; Schwarz US
Phys Rev E Stat Nonlin Soft Matter Phys; 2010 Mar; 81(3 Pt 1):030902. PubMed ID: 20365688
[TBL] [Abstract][Full Text] [Related]
11. Studying protein assembly with reversible Brownian dynamics of patchy particles.
Klein HC; Schwarz US
J Chem Phys; 2014 May; 140(18):184112. PubMed ID: 24832258
[TBL] [Abstract][Full Text] [Related]
12. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study.
Lindert S; Kekenes-Huskey PM; Huber G; Pierce L; McCammon JA
J Phys Chem B; 2012 Jul; 116(29):8449-59. PubMed ID: 22329450
[TBL] [Abstract][Full Text] [Related]
13. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics.
Vijaykumar A; Ouldridge TE; Ten Wolde PR; Bolhuis PG
J Chem Phys; 2017 Mar; 146(11):114106. PubMed ID: 28330367
[TBL] [Abstract][Full Text] [Related]
14. Multiscale Simulation of Receptor-Drug Association Kinetics: Application to Neuraminidase Inhibitors.
Zeller F; Luitz MP; Bomblies R; Zacharias M
J Chem Theory Comput; 2017 Oct; 13(10):5097-5105. PubMed ID: 28820938
[TBL] [Abstract][Full Text] [Related]
15. Computation of FRAP recovery times for linker histone - chromatin binding on the basis of Brownian dynamics simulations.
Öztürk MA; Wade RC
Biochim Biophys Acta Gen Subj; 2020 Oct; 1864(10):129653. PubMed ID: 32512172
[TBL] [Abstract][Full Text] [Related]
16. Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.
Viswanath S; Kreuzer SM; Cardenas AE; Elber R
J Chem Phys; 2013 Nov; 139(17):174105. PubMed ID: 24206285
[TBL] [Abstract][Full Text] [Related]
17. Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations.
Gabdoulline RR; Kummer U; Olsen LF; Wade RC
Biophys J; 2003 Sep; 85(3):1421-8. PubMed ID: 12944259
[TBL] [Abstract][Full Text] [Related]
18. DNA-protein binding rates: bending fluctuation and hydrodynamic coupling effects.
von Hansen Y; Netz RR; Hinczewski M
J Chem Phys; 2010 Apr; 132(13):135103. PubMed ID: 20387960
[TBL] [Abstract][Full Text] [Related]
19. A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly.
Chen J; Wu Y
Methods Mol Biol; 2018; 1764():401-411. PubMed ID: 29605930
[TBL] [Abstract][Full Text] [Related]
20. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.
Ray D; Gokey T; Mobley DL; Andricioaei I
J Chem Phys; 2020 Oct; 153(15):154117. PubMed ID: 33092382
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
