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175 related items for PubMed ID: 20949512

  • 1. Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N.
    Vorontsov II, Miyashita O.
    J Comput Chem; 2011 Apr 30; 32(6):1043-53. PubMed ID: 20949512
    [Abstract] [Full Text] [Related]

  • 2. Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose.
    Vorontsov II, Miyashita O.
    Biophys J; 2009 Nov 04; 97(9):2532-40. PubMed ID: 19883596
    [Abstract] [Full Text] [Related]

  • 3. The role of Glu41 in the binding of dimannose to P51G-m4-CVN.
    Ramadugu SK, Li Z, Kashyap HK, Margulis CJ.
    Biochemistry; 2014 Mar 11; 53(9):1477-84. PubMed ID: 24524298
    [Abstract] [Full Text] [Related]

  • 4. Potent inhibition of HIV-1 fusion by cyanovirin-N requires only a single high affinity carbohydrate binding site: characterization of low affinity carbohydrate binding site knockout mutants.
    Chang LC, Bewley CA.
    J Mol Biol; 2002 Apr 19; 318(1):1-8. PubMed ID: 12054763
    [Abstract] [Full Text] [Related]

  • 5. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.
    Ferrari AM, Degliesposti G, Sgobba M, Rastelli G.
    Bioorg Med Chem; 2007 Dec 15; 15(24):7865-77. PubMed ID: 17870536
    [Abstract] [Full Text] [Related]

  • 6. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
    Wittayanarakul K, Hannongbua S, Feig M.
    J Comput Chem; 2008 Apr 15; 29(5):673-85. PubMed ID: 17849388
    [Abstract] [Full Text] [Related]

  • 7. Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches.
    Srivastava HK, Sastry GN.
    J Chem Inf Model; 2012 Nov 26; 52(11):3088-98. PubMed ID: 23121465
    [Abstract] [Full Text] [Related]

  • 8. Computational study of the dynamics of mannose disaccharides free in solution and bound to the potent anti-HIV virucidal protein cyanovirin.
    Margulis CJ.
    J Phys Chem B; 2005 Mar 03; 109(8):3639-47. PubMed ID: 16851402
    [Abstract] [Full Text] [Related]

  • 9. Test MM-PB/SA on true conformational ensembles of protein-ligand complexes.
    Li Y, Liu Z, Wang R.
    J Chem Inf Model; 2010 Sep 27; 50(9):1682-92. PubMed ID: 20695488
    [Abstract] [Full Text] [Related]

  • 10. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.
    Rastelli G, Del Rio A, Degliesposti G, Sgobba M.
    J Comput Chem; 2010 Mar 27; 31(4):797-810. PubMed ID: 19569205
    [Abstract] [Full Text] [Related]

  • 11. A monovalent mutant of cyanovirin-N provides insight into the role of multiple interactions with gp120 for antiviral activity.
    Fromme R, Katiliene Z, Giomarelli B, Bogani F, Mc Mahon J, Mori T, Fromme P, Ghirlanda G.
    Biochemistry; 2007 Aug 14; 46(32):9199-207. PubMed ID: 17636873
    [Abstract] [Full Text] [Related]

  • 12. Molecular dynamics simulations of 2-amino-6-arylsulphonylbenzonitriles analogues as HIV inhibitors: interaction modes and binding free energies.
    Hu R, Barbault F, Maurel F, Delamar M, Zhang R.
    Chem Biol Drug Des; 2010 Dec 14; 76(6):518-26. PubMed ID: 20942836
    [Abstract] [Full Text] [Related]

  • 13. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
    Archontis G, Simonson T, Karplus M.
    J Mol Biol; 2001 Feb 16; 306(2):307-27. PubMed ID: 11237602
    [Abstract] [Full Text] [Related]

  • 14. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
    Genheden S, Ryde U.
    Proteins; 2012 May 16; 80(5):1326-42. PubMed ID: 22274991
    [Abstract] [Full Text] [Related]

  • 15. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations.
    Rizzo RC, Toba S, Kuntz ID.
    J Med Chem; 2004 Jun 03; 47(12):3065-74. PubMed ID: 15163188
    [Abstract] [Full Text] [Related]

  • 16. Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer.
    Freedman H, Huynh LP, Le L, Cheatham TE, Tuszynski JA, Truong TN.
    J Phys Chem B; 2010 Feb 18; 114(6):2227-37. PubMed ID: 20099932
    [Abstract] [Full Text] [Related]

  • 17. 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 30; 23(2):214-21. PubMed ID: 11924735
    [Abstract] [Full Text] [Related]

  • 18. Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.
    Zuo Z, Gandhi NS, Mancera RL.
    J Chem Inf Model; 2010 Dec 27; 50(12):2201-12. PubMed ID: 21090792
    [Abstract] [Full Text] [Related]

  • 19. Calculation of protein-ligand binding free energy using smooth reaction path generation (SRPG) method: a comparison of the explicit water model, gb/sa model and docking score function.
    Mitomo D, Fukunishi Y, Higo J, Nakamura H.
    Genome Inform; 2009 Oct 27; 23(1):85-97. PubMed ID: 20180264
    [Abstract] [Full Text] [Related]

  • 20. Dissecting carbohydrate-Cyanovirin-N binding by structure-guided mutagenesis: functional implications for viral entry inhibition.
    Barrientos LG, Matei E, Lasala F, Delgado R, Gronenborn AM.
    Protein Eng Des Sel; 2006 Dec 27; 19(12):525-35. PubMed ID: 17012344
    [Abstract] [Full Text] [Related]

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