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231 related items for PubMed ID: 12112673
1. Assessing equilibration and convergence in biomolecular simulations. Smith LJ, Daura X, van Gunsteren WF. Proteins; 2002 Aug 15; 48(3):487-96. PubMed ID: 12112673 [Abstract] [Full Text] [Related]
2. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. Periole X, Mark AE. J Chem Phys; 2007 Jan 07; 126(1):014903. PubMed ID: 17212515 [Abstract] [Full Text] [Related]
3. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations. Kannan S, Zacharias M. Proteins; 2009 Aug 01; 76(2):448-60. PubMed ID: 19173315 [Abstract] [Full Text] [Related]
4. Molecular dynamics simulations of peptide fragments from hen lysozyme: insight into non-native protein conformations. Smith LJ, Mark AE, Dobson CM, van Gunsteren WF. J Mol Biol; 1998 Jul 24; 280(4):703-19. PubMed ID: 9677298 [Abstract] [Full Text] [Related]
5. 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 01; 51(1):109-25. PubMed ID: 12596268 [Abstract] [Full Text] [Related]
6. On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study. Glättli A, Daura X, Bindschädler P, Jaun B, Mahajan YR, Mathad RI, Rueping M, Seebach D, van Gunsteren WF. Chemistry; 2005 Dec 09; 11(24):7276-93. PubMed ID: 16247825 [Abstract] [Full Text] [Related]
7. Conformational dynamics of cytochrome c: correlation to hydrogen exchange. García AE, Hummer G. Proteins; 1999 Aug 01; 36(2):175-91. PubMed ID: 10398365 [Abstract] [Full Text] [Related]
8. Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore. Mihailescu D, Reed J, Smith JC. Biopolymers; 2003 Oct 01; 70(2):121-33. PubMed ID: 14517902 [Abstract] [Full Text] [Related]
9. Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer. Gee PJ, van Gunsteren WF. Chemistry; 2005 Dec 16; 12(1):72-5. PubMed ID: 16259034 [Abstract] [Full Text] [Related]
10. Molecular dynamics simulation of folding of a short helical peptide with many charged residues. Wei CC, Ho MH, Wang WH, Sun YC. J Phys Chem B; 2005 Oct 27; 109(42):19980-6. PubMed ID: 16853583 [Abstract] [Full Text] [Related]
11. Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model. Smith AV, Hall CK. J Mol Biol; 2001 Sep 07; 312(1):187-202. PubMed ID: 11545596 [Abstract] [Full Text] [Related]
12. beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution. Santiveri CM, Jiménez MA, Rico M, Van Gunsteren WF, Daura X. J Pept Sci; 2004 Sep 07; 10(9):546-65. PubMed ID: 15473263 [Abstract] [Full Text] [Related]
13. Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters. Ikebe J, Kamiya N, Ito J, Shindo H, Higo J. Protein Sci; 2007 Aug 07; 16(8):1596-608. PubMed ID: 17656579 [Abstract] [Full Text] [Related]
14. Comparative study of generalized born models: Born radii and peptide folding. Zhu J, Alexov E, Honig B. J Phys Chem B; 2005 Feb 24; 109(7):3008-22. PubMed ID: 16851315 [Abstract] [Full Text] [Related]
15. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. Graf J, Nguyen PH, Stock G, Schwalbe H. J Am Chem Soc; 2007 Feb 07; 129(5):1179-89. PubMed ID: 17263399 [Abstract] [Full Text] [Related]
16. Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations. Soto P, Colombo G. Proteins; 2004 Dec 01; 57(4):734-46. PubMed ID: 15390268 [Abstract] [Full Text] [Related]
17. Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide. Gattin Z, van Gunsteren WF. J Phys Chem B; 2009 Jun 25; 113(25):8695-703. PubMed ID: 19485309 [Abstract] [Full Text] [Related]
18. Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions. Reif MM, Kräutler V, Kastenholz MA, Daura X, Hünenberger PH. J Phys Chem B; 2009 Mar 12; 113(10):3112-28. PubMed ID: 19228001 [Abstract] [Full Text] [Related]
19. Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue. Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. J Phys Chem B; 2008 May 01; 112(17):5439-48. PubMed ID: 18402479 [Abstract] [Full Text] [Related]