195 related articles for article (PubMed ID: 22278814)
1. Potential of mean force of water-proton bath and molecular dynamic simulation of proteins at constant pH.
Vorobjev YN
J Comput Chem; 2012 Mar; 33(8):832-42. PubMed ID: 22278814
[TBL] [Abstract][Full Text] [Related]
2. [Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration].
Vorob'ev IuN
Mol Biol (Mosk); 2011; 45(2):346-55. PubMed ID: 21634122
[TBL] [Abstract][Full Text] [Related]
3. Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH.
Vorobjev YN
Adv Protein Chem Struct Biol; 2011; 85():281-322. PubMed ID: 21920327
[TBL] [Abstract][Full Text] [Related]
4. 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]
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. Biasing the center of charge in molecular dynamics simulations with empirical valence bond models: free energetics of an excess proton in a water droplet.
Köfinger J; Dellago C
J Phys Chem B; 2008 Feb; 112(8):2349-56. PubMed ID: 18247589
[TBL] [Abstract][Full Text] [Related]
7. Dynamics of proton transfer and vibrational relaxation in dilute hydrofluoric acid.
Joutsuka T; Ando K
J Phys Chem A; 2011 Feb; 115(5):678-84. PubMed ID: 21210667
[TBL] [Abstract][Full Text] [Related]
8. A polarizable reactive force field for water to enable molecular dynamics simulations of proton transport.
Asthana A; Wheeler DR
J Chem Phys; 2013 May; 138(17):174502. PubMed ID: 23656139
[TBL] [Abstract][Full Text] [Related]
9. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration.
Baptista AM; Martel PJ; Petersen SB
Proteins; 1997 Apr; 27(4):523-44. PubMed ID: 9141133
[TBL] [Abstract][Full Text] [Related]
10. Constant pH molecular dynamics in generalized Born implicit solvent.
Mongan J; Case DA; McCammon JA
J Comput Chem; 2004 Dec; 25(16):2038-48. PubMed ID: 15481090
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. Free energy of proton binding in proteins.
Poland D
Biopolymers; 2003 May; 69(1):60-71. PubMed ID: 12717722
[TBL] [Abstract][Full Text] [Related]
13. A generalized reactive force field for nonlinear hydrogen bonds: hydrogen dynamics and transfer in malonaldehyde.
Yang Y; Meuwly M
J Chem Phys; 2010 Aug; 133(6):064503. PubMed ID: 20707571
[TBL] [Abstract][Full Text] [Related]
14. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.
Wang J; Tan C; Chanco E; Luo R
Phys Chem Chem Phys; 2010 Feb; 12(5):1194-202. PubMed ID: 20094685
[TBL] [Abstract][Full Text] [Related]
15. The combined simulation approach of atomistic and continuum models for the thermodynamics of lysozyme crystals.
Chang J; Lenhoff AM; Sandler SI
J Phys Chem B; 2005 Oct; 109(41):19507-15. PubMed ID: 16853520
[TBL] [Abstract][Full Text] [Related]
16. Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center.
Sham YY; Muegge I; Warshel A
Proteins; 1999 Sep; 36(4):484-500. PubMed ID: 10450091
[TBL] [Abstract][Full Text] [Related]
17. Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
Simonson T; Carlsson J; Case DA
J Am Chem Soc; 2004 Apr; 126(13):4167-80. PubMed ID: 15053606
[TBL] [Abstract][Full Text] [Related]
18. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.
Takemura K; Guo H; Sakuraba S; Matubayasi N; Kitao A
J Chem Phys; 2012 Dec; 137(21):215105. PubMed ID: 23231264
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study.
Długosz M; Antosiewicz JM
J Phys Chem B; 2005 Jul; 109(28):13777-84. PubMed ID: 16852726
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]