188 related articles for article (PubMed ID: 20942836)
21. Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases.
Sadiq SK; Wright DW; Kenway OA; Coveney PV
J Chem Inf Model; 2010 May; 50(5):890-905. PubMed ID: 20384328
[TBL] [Abstract][Full Text] [Related]
22. Bridge water mediates nevirapine binding to wild type and Y181C HIV-1 reverse transcriptase--evidence from molecular dynamics simulations and MM-PBSA calculations.
Treesuwan W; Hannongbua S
J Mol Graph Model; 2009; 27(8):921-9. PubMed ID: 19414275
[TBL] [Abstract][Full Text] [Related]
23. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.
Pérez C; Pastor M; Ortiz AR; Gago F
J Med Chem; 1998 Mar; 41(6):836-52. PubMed ID: 9526559
[TBL] [Abstract][Full Text] [Related]
24. Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS.
Zhou Z; Madura JD
Proteins; 2004 Nov; 57(3):493-503. PubMed ID: 15382241
[TBL] [Abstract][Full Text] [Related]
25. 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; 32(6):1043-53. PubMed ID: 20949512
[TBL] [Abstract][Full Text] [Related]
26. Predicting binding modes from free energy calculations.
Nervall M; Hanspers P; Carlsson J; Boukharta L; Aqvist J
J Med Chem; 2008 May; 51(9):2657-67. PubMed ID: 18410080
[TBL] [Abstract][Full Text] [Related]
27. Molecular dynamics simulations of the three dimensional model of plasmepsin II-peptidic inhibitor complexes.
Pranav Kumar SK; Kulkarni VM
Drug Des Discov; 2001; 17(4):293-313. PubMed ID: 11765133
[TBL] [Abstract][Full Text] [Related]
28. 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]
29. Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: atomistic and coarse-grained simulations.
Cheng Y; Li D; Ji B; Shi X; Gao H
J Mol Graph Model; 2010 Sep; 29(2):171-7. PubMed ID: 20580296
[TBL] [Abstract][Full Text] [Related]
30. Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors.
Li D; Liu MS; Ji B; Hwang K; Huang Y
J Chem Phys; 2009 Jun; 130(21):215102. PubMed ID: 19508101
[TBL] [Abstract][Full Text] [Related]
31. Theoretical studies of HIV-1 reverse transcriptase inhibition.
Świderek K; Martí S; Moliner V
Phys Chem Chem Phys; 2012 Sep; 14(36):12614-24. PubMed ID: 22820901
[TBL] [Abstract][Full Text] [Related]
32. Receptor- and ligand-based 3D-QSAR study for a series of non-nucleoside HIV-1 reverse transcriptase inhibitors.
Hu R; Barbault F; Delamar M; Zhang R
Bioorg Med Chem; 2009 Mar; 17(6):2400-9. PubMed ID: 19250835
[TBL] [Abstract][Full Text] [Related]
33. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.
Stoica I; Sadiq SK; Coveney PV
J Am Chem Soc; 2008 Feb; 130(8):2639-48. PubMed ID: 18225901
[TBL] [Abstract][Full Text] [Related]
34. Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations.
Eriksson MA; Pitera J; Kollman PA
J Med Chem; 1999 Mar; 42(5):868-81. PubMed ID: 10072684
[TBL] [Abstract][Full Text] [Related]
35. Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.
Cui Q; Sulea T; Schrag JD; Munger C; Hung MN; Naïm M; Cygler M; Purisima EO
J Mol Biol; 2008 Jun; 379(4):787-802. PubMed ID: 18479705
[TBL] [Abstract][Full Text] [Related]
36. 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]
37. Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment.
Strockbine B; Rizzo RC
Proteins; 2007 May; 67(3):630-42. PubMed ID: 17335007
[TBL] [Abstract][Full Text] [Related]
38. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method.
Smith RH; Jorgensen WL; Tirado-Rives J; Lamb ML; Janssen PA; Michejda CJ; Kroeger Smith MB
J Med Chem; 1998 Dec; 41(26):5272-86. PubMed ID: 9857095
[TBL] [Abstract][Full Text] [Related]
39. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods.
Adekoya OA; Willassen NP; Sylte I
J Struct Biol; 2006 Feb; 153(2):129-44. PubMed ID: 16376106
[TBL] [Abstract][Full Text] [Related]
40. Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations.
Wittayanarakul K; Aruksakunwong O; Sompornpisut P; Sanghiran-Lee V; Parasuk V; Pinitglang S; Hannongbua S
J Chem Inf Model; 2005; 45(2):300-8. PubMed ID: 15807491
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
