325 related articles for article (PubMed ID: 16471699)
1. Solvation model based on order parameters and a fast sampling method for the calculation of the solvation free energies of peptides.
Gu C; Lustig S; Trout BL
J Phys Chem B; 2006 Jan; 110(3):1476-84. PubMed ID: 16471699
[TBL] [Abstract][Full Text] [Related]
2. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.
Wimley WC; Creamer TP; White SH
Biochemistry; 1996 Apr; 35(16):5109-24. PubMed ID: 8611495
[TBL] [Abstract][Full Text] [Related]
3. The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method.
Xie L; Liu H
J Comput Chem; 2002 Nov; 23(15):1404-15. PubMed ID: 12370943
[TBL] [Abstract][Full Text] [Related]
4. A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation.
Efremov RG; Nolde DE; Vergoten G; Arseniev AS
Biophys J; 1999 May; 76(5):2448-59. PubMed ID: 10233062
[TBL] [Abstract][Full Text] [Related]
5. Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking.
Totrov M
J Comput Chem; 2004 Mar; 25(4):609-19. PubMed ID: 14735578
[TBL] [Abstract][Full Text] [Related]
6. Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.
Guvench O; Weiser J; Shenkin P; Kolossváry I; Still WC
J Comput Chem; 2002 Jan; 23(2):214-21. PubMed ID: 11924735
[TBL] [Abstract][Full Text] [Related]
7. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
Marenich AV; Cramer CJ; Truhlar DG
J Phys Chem B; 2009 May; 113(18):6378-96. PubMed ID: 19366259
[TBL] [Abstract][Full Text] [Related]
8. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
Shirts MR; Pande VS
J Chem Phys; 2005 Apr; 122(13):134508. PubMed ID: 15847482
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Are solvation free energies of homogeneous helical peptides additive?
Staritzbichler R; Gu W; Helms V
J Phys Chem B; 2005 Oct; 109(40):19000-7. PubMed ID: 16853446
[TBL] [Abstract][Full Text] [Related]
11. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
Pitera JW; Kollman PA
Proteins; 2000 Nov; 41(3):385-97. PubMed ID: 11025549
[TBL] [Abstract][Full Text] [Related]
12. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
Geerke DP; van Gunsteren WF
J Phys Chem B; 2007 Jun; 111(23):6425-36. PubMed ID: 17508737
[TBL] [Abstract][Full Text] [Related]
13. Implicit nonpolar solvent models.
Tan C; Tan YH; Luo R
J Phys Chem B; 2007 Oct; 111(42):12263-74. PubMed ID: 17918880
[TBL] [Abstract][Full Text] [Related]
14. Polyproline II helix is the preferred conformation for unfolded polyalanine in water.
Mezei M; Fleming PJ; Srinivasan R; Rose GD
Proteins; 2004 May; 55(3):502-7. PubMed ID: 15103614
[TBL] [Abstract][Full Text] [Related]
15. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
Pei J; Wang Q; Zhou J; Lai L
Proteins; 2004 Dec; 57(4):651-64. PubMed ID: 15390269
[TBL] [Abstract][Full Text] [Related]
16. Hydration free energies of amino acids: why side chain analog data are not enough.
König G; Boresch S
J Phys Chem B; 2009 Jul; 113(26):8967-74. PubMed ID: 19507836
[TBL] [Abstract][Full Text] [Related]
17. Improving the performance of the coupled reference interaction site model-hyper-netted chain (RISM-HNC)/simulation method for free energy of solvation.
Freedman H; Le L; Tuszynski JA; Truong TN
J Phys Chem B; 2008 Feb; 112(8):2340-8. PubMed ID: 18251537
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Rational design of ion force fields based on thermodynamic solvation properties.
Horinek D; Mamatkulov SI; Netz RR
J Chem Phys; 2009 Mar; 130(12):124507. PubMed ID: 19334851
[TBL] [Abstract][Full Text] [Related]
20. Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.
Totrov M; Abagyan R
Biopolymers; 2001; 60(2):124-33. PubMed ID: 11455546
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]