359 related articles for article (PubMed ID: 26626529)
1. Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model.
Okur A; Wickstrom L; Layten M; Geney R; Song K; Hornak V; Simmerling C
J Chem Theory Comput; 2006 Mar; 2(2):420-33. PubMed ID: 26626529
[TBL] [Abstract][Full Text] [Related]
2. Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models.
Okur A; Wickstrom L; Simmerling C
J Chem Theory Comput; 2008 Mar; 4(3):488-98. PubMed ID: 26620789
[TBL] [Abstract][Full Text] [Related]
3. Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method.
Chaudhury S; Olson MA; Tawa G; Wallqvist A; Lee MS
J Chem Theory Comput; 2012 Feb; 8(2):677-87. PubMed ID: 26596615
[TBL] [Abstract][Full Text] [Related]
4. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation.
Yu Y; Wang J; Shao Q; Shi J; Zhu W
J Chem Phys; 2015 Mar; 142(12):125105. PubMed ID: 25833612
[TBL] [Abstract][Full Text] [Related]
5. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.
Roe DR; Okur A; Wickstrom L; Hornak V; Simmerling C
J Phys Chem B; 2007 Feb; 111(7):1846-57. PubMed ID: 17256983
[TBL] [Abstract][Full Text] [Related]
6. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
Periole X; Mark AE
J Chem Phys; 2007 Jan; 126(1):014903. PubMed ID: 17212515
[TBL] [Abstract][Full Text] [Related]
7. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
Zhou R
Proteins; 2003 Nov; 53(2):148-61. PubMed ID: 14517967
[TBL] [Abstract][Full Text] [Related]
8. Does Replica Exchange with Solute Tempering Efficiently Sample Aβ Peptide Conformational Ensembles?
Smith AK; Lockhart C; Klimov DK
J Chem Theory Comput; 2016 Oct; 12(10):5201-5214. PubMed ID: 27560127
[TBL] [Abstract][Full Text] [Related]
9. Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics.
Sharma P; Singh P; Bisetty K; Rodriguez A; Perez JJ
J Pept Sci; 2011 Mar; 17(3):174-83. PubMed ID: 20878681
[TBL] [Abstract][Full Text] [Related]
10. Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir.
Okur A; Roe DR; Cui G; Hornak V; Simmerling C
J Chem Theory Comput; 2007 Mar; 3(2):557-68. PubMed ID: 26637035
[TBL] [Abstract][Full Text] [Related]
11. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
Kannan S; Zacharias M
Proteins; 2010 Oct; 78(13):2809-19. PubMed ID: 20635348
[TBL] [Abstract][Full Text] [Related]
12. Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs.
Geist N; Kulke M; Schulig L; Link A; Langel W
J Phys Chem B; 2019 Jul; 123(28):5995-6006. PubMed ID: 31265293
[TBL] [Abstract][Full Text] [Related]
13. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
Vorobjev YN; Almagro JC; Hermans J
Proteins; 1998 Sep; 32(4):399-413. PubMed ID: 9726412
[TBL] [Abstract][Full Text] [Related]
14. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
Deng N; Zhang BW; Levy RM
J Chem Theory Comput; 2015 Jun; 11(6):2868-78. PubMed ID: 26236174
[TBL] [Abstract][Full Text] [Related]
15. TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent.
Li X; Snyder JA; Stuart SJ; Latour RA
J Chem Phys; 2015 Oct; 143(14):144105. PubMed ID: 26472361
[TBL] [Abstract][Full Text] [Related]
16. Convergence of replica exchange molecular dynamics.
Zhang W; Wu C; Duan Y
J Chem Phys; 2005 Oct; 123(15):154105. PubMed ID: 16252940
[TBL] [Abstract][Full Text] [Related]
17. Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations.
Abraham MJ; Gready JE
J Chem Theory Comput; 2008 Jul; 4(7):1119-28. PubMed ID: 26636365
[TBL] [Abstract][Full Text] [Related]
18. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.
Beck DA; White GW; Daggett V
J Struct Biol; 2007 Mar; 157(3):514-23. PubMed ID: 17113307
[TBL] [Abstract][Full Text] [Related]
19. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
Hassan SA; Mehler EL; Zhang D; Weinstein H
Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268
[TBL] [Abstract][Full Text] [Related]
20. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.
Chebaro Y; Dong X; Laghaei R; Derreumaux P; Mousseau N
J Phys Chem B; 2009 Jan; 113(1):267-74. PubMed ID: 19067549
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]