167 related articles for article (PubMed ID: 11562944)
1. Protein molecular dynamics with the generalized Born/ACE solvent model.
Calimet N; Schaefer M; Simonson T
Proteins; 2001 Nov; 45(2):144-58. PubMed ID: 11562944
[TBL] [Abstract][Full Text] [Related]
2. Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization.
Zhang H; Tan T; van der Spoel D
J Chem Theory Comput; 2015 Nov; 11(11):5103-13. PubMed ID: 26574308
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
Katkova EV; Onufriev AV; Aguilar B; Sulimov VB
J Mol Graph Model; 2017 Mar; 72():70-80. PubMed ID: 28064081
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. Exploring protein native states and large-scale conformational changes with a modified generalized born model.
Onufriev A; Bashford D; Case DA
Proteins; 2004 May; 55(2):383-94. PubMed ID: 15048829
[TBL] [Abstract][Full Text] [Related]
7. An n log n Generalized Born Approximation.
Anandakrishnan R; Daga M; Onufriev AV
J Chem Theory Comput; 2011 Mar; 7(3):544-59. PubMed ID: 26596289
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.
Moulinier L; Case DA; Simonson T
Acta Crystallogr D Biol Crystallogr; 2003 Dec; 59(Pt 12):2094-103. PubMed ID: 14646067
[TBL] [Abstract][Full Text] [Related]
10. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water.
Xia B; Tsui V; Case DA; Dyson HJ; Wright PE
J Biomol NMR; 2002 Apr; 22(4):317-31. PubMed ID: 12018480
[TBL] [Abstract][Full Text] [Related]
11. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
Olson MA
Proteins; 2004 Dec; 57(4):645-50. PubMed ID: 15481087
[TBL] [Abstract][Full Text] [Related]
12. FACTS: Fast analytical continuum treatment of solvation.
Haberthür U; Caflisch A
J Comput Chem; 2008 Apr; 29(5):701-15. PubMed ID: 17918282
[TBL] [Abstract][Full Text] [Related]
13. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
Li X; Hassan SA; Mehler EL
Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866
[TBL] [Abstract][Full Text] [Related]
14. Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer.
Król M
J Comput Chem; 2003 Apr; 24(5):531-46. PubMed ID: 12632469
[TBL] [Abstract][Full Text] [Related]
15. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
Gohlke H; Case DA
J Comput Chem; 2004 Jan; 25(2):238-50. PubMed ID: 14648622
[TBL] [Abstract][Full Text] [Related]
16. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.
Vorobjev YN; Hermans J
Biophys Chem; 1999 Apr; 78(1-2):195-205. PubMed ID: 10343388
[TBL] [Abstract][Full Text] [Related]
17. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.
Yeh IC; Lee MS; Olson MA
J Phys Chem B; 2008 Nov; 112(47):15064-73. PubMed ID: 18959439
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. The use of a generalized born model for the analysis of protein conformational transitions: a comparative study with explicit solvent simulations for chemotaxis Y protein (CheY).
Formaneck MS; Cui Q
J Comput Chem; 2006 Dec; 27(16):1923-43. PubMed ID: 17019722
[TBL] [Abstract][Full Text] [Related]
20. Comparative study of generalized born models: Born radii and peptide folding.
Zhu J; Alexov E; Honig B
J Phys Chem B; 2005 Feb; 109(7):3008-22. PubMed ID: 16851315
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
