These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

153 related articles for article (PubMed ID: 21117688)

  • 1. Practical considerations for building GROMOS-compatible small-molecule topologies.
    Lemkul JA; Allen WJ; Bevan DR
    J Chem Inf Model; 2010 Dec; 50(12):2221-35. PubMed ID: 21117688
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions.
    Ricci CG; de Andrade AS; Mottin M; Netz PA
    J Phys Chem B; 2010 Aug; 114(30):9882-93. PubMed ID: 20614923
    [TBL] [Abstract][Full Text] [Related]  

  • 3. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.
    Malde AK; Zuo L; Breeze M; Stroet M; Poger D; Nair PC; Oostenbrink C; Mark AE
    J Chem Theory Comput; 2011 Dec; 7(12):4026-37. PubMed ID: 26598349
    [TBL] [Abstract][Full Text] [Related]  

  • 4. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.
    Oostenbrink C; Villa A; Mark AE; van Gunsteren WF
    J Comput Chem; 2004 Oct; 25(13):1656-76. PubMed ID: 15264259
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
    Arnautova YA; Jagielska A; Scheraga HA
    J Phys Chem B; 2006 Mar; 110(10):5025-44. PubMed ID: 16526746
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Combination of the CHARMM27 force field with united-atom lipid force fields.
    Sapay N; Tieleman DP
    J Comput Chem; 2011 May; 32(7):1400-10. PubMed ID: 21425293
    [TBL] [Abstract][Full Text] [Related]  

  • 7. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
    Schüttelkopf AW; van Aalten DM
    Acta Crystallogr D Biol Crystallogr; 2004 Aug; 60(Pt 8):1355-63. PubMed ID: 15272157
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore.
    Kaminski S; Daminelli G; Mroginski MA
    J Phys Chem B; 2009 Jan; 113(4):945-58. PubMed ID: 19123828
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Comparison of protein force fields for molecular dynamics simulations.
    Guvench O; MacKerell AD
    Methods Mol Biol; 2008; 443():63-88. PubMed ID: 18446282
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances.
    Cézard C; Trivelli X; Aubry F; Djedaïni-Pilard F; Dupradeau FY
    Phys Chem Chem Phys; 2011 Sep; 13(33):15103-21. PubMed ID: 21792425
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Charge group partitioning in biomolecular simulation.
    Canzar S; El-Kebir M; Pool R; Elbassioni K; Mark AE; Geerke DP; Stougie L; Klau GW
    J Comput Biol; 2013 Mar; 20(3):188-98. PubMed ID: 23461571
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
    Mobley DL; Dumont E; Chodera JD; Dill KA
    J Phys Chem B; 2007 Mar; 111(9):2242-54. PubMed ID: 17291029
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.
    Okur A; Strockbine B; Hornak V; Simmerling C
    J Comput Chem; 2003 Jan; 24(1):21-31. PubMed ID: 12483672
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.
    Spacková N; Réblová K; Sponer J
    J Phys Chem B; 2010 Aug; 114(32):10581-93. PubMed ID: 20701388
    [TBL] [Abstract][Full Text] [Related]  

  • 15. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
    Villa A; Fan H; Wassenaar T; Mark AE
    J Phys Chem B; 2007 May; 111(21):6015-25. PubMed ID: 17489626
    [TBL] [Abstract][Full Text] [Related]  

  • 16. An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems.
    Shi S; Yan L; Yang Y; Fisher-Shaulsky J; Thacher T
    J Comput Chem; 2003 Jul; 24(9):1059-76. PubMed ID: 12759906
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.
    de Hatten X; Cournia Z; Huc I; Smith JC; Metzler-Nolte N
    Chemistry; 2007; 13(29):8139-52. PubMed ID: 17763506
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data.
    Stocker U; van Gunsteren WF
    Proteins; 2000 Jul; 40(1):145-53. PubMed ID: 10813839
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Conformation, dynamics, solvation and relative stabilities of selected beta-hexopyranoses in water: a molecular dynamics study with the GROMOS 45A4 force field.
    Kräutler V; Müller M; Hünenberger PH
    Carbohydr Res; 2007 Oct; 342(14):2097-124. PubMed ID: 17573054
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A new GROMOS force field for hexopyranose-based carbohydrates.
    Lins RD; Hünenberger PH
    J Comput Chem; 2005 Oct; 26(13):1400-12. PubMed ID: 16035088
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.