BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

123 related articles for article (PubMed ID: 10336384)

  • 1. Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study.
    Wang J; Dixon R; Kollman PA
    Proteins; 1999 Jan; 34(1):69-81. PubMed ID: 10336384
    [TBL] [Abstract][Full Text] [Related]  

  • 2. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
    Wang W; Wang J; Kollman PA
    Proteins; 1999 Feb; 34(3):395-402. PubMed ID: 10024025
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Contributions to the binding free energy of ligands to avidin and streptavidin.
    Lazaridis T; Masunov A; Gandolfo F
    Proteins; 2002 May; 47(2):194-208. PubMed ID: 11933066
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S; Kollman PA
    Proteins; 1993 Jul; 16(3):226-45. PubMed ID: 8346190
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding.
    Tong Y; Mei Y; Li YL; Ji CG; Zhang JZ
    J Am Chem Soc; 2010 Apr; 132(14):5137-42. PubMed ID: 20302307
    [TBL] [Abstract][Full Text] [Related]  

  • 6. New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex.
    General IJ; Dragomirova R; Meirovitch H
    J Phys Chem B; 2011 Jan; 115(1):168-75. PubMed ID: 21158467
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin.
    Dixon RW; Radmer RJ; Kuhn B; Kollman PA; Yang J; Raposo C; Wilcox CS; Klumb LA; Stayton PS; Behnke C; Le Trong I; Stenkamp R
    J Org Chem; 2002 Mar; 67(6):1827-37. PubMed ID: 11895399
    [TBL] [Abstract][Full Text] [Related]  

  • 8. How to obtain statistically converged MM/GBSA results.
    Genheden S; Ryde U
    J Comput Chem; 2010 Mar; 31(4):837-46. PubMed ID: 19598265
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Absolute free energy of binding of avidin/biotin, revisited.
    General IJ; Dragomirova R; Meirovitch H
    J Phys Chem B; 2012 Jun; 116(23):6628-36. PubMed ID: 22300239
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models.
    Kuhn B; Kollman PA
    J Med Chem; 2000 Oct; 43(20):3786-91. PubMed ID: 11020294
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Conformational dependence of charges in protein simulations.
    Söderhjelm P; Ryde U
    J Comput Chem; 2009 Apr; 30(5):750-60. PubMed ID: 18773405
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.
    Weis A; Katebzadeh K; Söderhjelm P; Nilsson I; Ryde U
    J Med Chem; 2006 Nov; 49(22):6596-606. PubMed ID: 17064078
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
    Genheden S; Ryde U
    Proteins; 2012 May; 80(5):1326-42. PubMed ID: 22274991
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Conformational flexibility of avidin: the influence of biotin binding.
    Celej MS; Montich GG; Fidelio GD
    Biochem Biophys Res Commun; 2004 Dec; 325(3):922-7. PubMed ID: 15541378
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY; Chu ZT; Tao H; Warshel A
    Proteins; 2000 Jun; 39(4):393-407. PubMed ID: 10813821
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Structural investigation of the interactions of biotinylruthenocene with avidin.
    Strzelczyk P; Bujacz A; Plażuk D; Zakrzewski J; Bujacz G
    Chem Biol Interact; 2013 Jun; 204(1):6-12. PubMed ID: 23603015
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
    Genheden S; Mikulskis P; Hu L; Kongsted J; Söderhjelm P; Ryde U
    J Am Chem Soc; 2011 Aug; 133(33):13081-92. PubMed ID: 21728337
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties.
    Brandt T; Holzmann N; Muley L; Khayat M; Wegscheid-Gerlach C; Baum B; Heine A; Hangauer D; Klebe G
    J Mol Biol; 2011 Feb; 405(5):1170-87. PubMed ID: 21111747
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Aromatic side-chain cluster of biotin binding site of avidin allows circular dichroism spectroscopic investigation of its ligand binding properties.
    Zsila F
    J Mol Recognit; 2011; 24(6):995-1006. PubMed ID: 22038806
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Estimates of ligand-binding affinities supported by quantum mechanical methods.
    Söderhjelm P; Kongsted J; Genheden S; Ryde U
    Interdiscip Sci; 2010 Mar; 2(1):21-37. PubMed ID: 20640794
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.