192 related articles for article (PubMed ID: 12564936)
1. Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease.
Zhu Z; Schuster DI; Tuckerman ME
Biochemistry; 2003 Feb; 42(5):1326-33. PubMed ID: 12564936
[TBL] [Abstract][Full Text] [Related]
2. Structural analysis of lead fullerene-based inhibitor bound to human immunodeficiency virus type 1 protease in solution from molecular dynamics simulations.
Lee VS; Nimmanpipug P; Aruksakunwong O; Promsri S; Sompornpisut P; Hannongbua S
J Mol Graph Model; 2007 Sep; 26(2):558-70. PubMed ID: 17468026
[TBL] [Abstract][Full Text] [Related]
3. Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations.
Durdagi S; Mavromoustakos T; Chronakis N; Papadopoulos MG
Bioorg Med Chem; 2008 Dec; 16(23):9957-74. PubMed ID: 18996019
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.
Lepsík M; Kríz Z; Havlas Z
Proteins; 2004 Nov; 57(2):279-93. PubMed ID: 15340915
[TBL] [Abstract][Full Text] [Related]
6. Structural and dynamical properties of different protonated states of mutant HIV-1 protease complexed with the saquinavir inhibitor studied by molecular dynamics simulations.
Aruksakunwong O; Wittayanarakul K; Sompornpisut P; Sanghiran V; Parasuk V; Hannongbua S
J Mol Graph Model; 2006 Nov; 25(3):324-32. PubMed ID: 16504560
[TBL] [Abstract][Full Text] [Related]
7. 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; 29(5):673-85. PubMed ID: 17849388
[TBL] [Abstract][Full Text] [Related]
8. Structural and electronic properties of new fullerene derivatives and their possible application as HIV-1 protease inhibitors.
Ibrahim M; Saleh NA; Hameed AJ; Elshemey WM; Elsayed AA
Spectrochim Acta A Mol Biomol Spectrosc; 2010 Feb; 75(2):702-9. PubMed ID: 20044306
[TBL] [Abstract][Full Text] [Related]
9. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes.
Lu Y; Yang CY; Wang S
J Am Chem Soc; 2006 Sep; 128(36):11830-9. PubMed ID: 16953623
[TBL] [Abstract][Full Text] [Related]
10. Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations.
Verkhivker GM
Pac Symp Biocomput; 1996; ():638-52. PubMed ID: 9390264
[TBL] [Abstract][Full Text] [Related]
11. Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps.
Leonis G; Czyżnikowska Ż; Megariotis G; Reis H; Papadopoulos MG
J Chem Inf Model; 2012 Jun; 52(6):1542-58. PubMed ID: 22587384
[TBL] [Abstract][Full Text] [Related]
12. Molecular dynamics simulations of ligand-induced flap closing in HIV-1 protease approach X-ray resolution: establishing the role of bound water in the flap closing mechanism.
Singh G; Senapati S
Biochemistry; 2008 Oct; 47(40):10657-64. PubMed ID: 18785756
[TBL] [Abstract][Full Text] [Related]
13. A molecular dynamics study comparing a wild-type with a multiple drug resistant HIV protease: differences in flap and aspartate 25 cavity dimensions.
Seibold SA; Cukier RI
Proteins; 2007 Nov; 69(3):551-65. PubMed ID: 17623840
[TBL] [Abstract][Full Text] [Related]
14. 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]
15. Resistant mechanism against nelfinavir of human immunodeficiency virus type 1 proteases.
Ode H; Ota M; Neya S; Hata M; Sugiura W; Hoshino T
J Phys Chem B; 2005 Jan; 109(1):565-74. PubMed ID: 16851048
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance.
Hou T; Yu R
J Med Chem; 2007 Mar; 50(6):1177-88. PubMed ID: 17300185
[TBL] [Abstract][Full Text] [Related]
18. Molecular dynamics and free energy studies on the wild-type and mutated HIV-1 protease complexed with four approved drugs: mechanism of binding and drug resistance.
Alcaro S; Artese A; Ceccherini-Silberstein F; Ortuso F; Perno CF; Sing T; Svicher V
J Chem Inf Model; 2009 Jul; 49(7):1751-61. PubMed ID: 19537723
[TBL] [Abstract][Full Text] [Related]
19. Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants.
Kozísek M; Bray J; Rezácová P; Sasková K; Brynda J; Pokorná J; Mammano F; Rulísek L; Konvalinka J
J Mol Biol; 2007 Dec; 374(4):1005-16. PubMed ID: 17977555
[TBL] [Abstract][Full Text] [Related]
20. Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design.
Perryman AL; Lin JH; McCammon JA
Biopolymers; 2006 Jun; 82(3):272-84. PubMed ID: 16508951
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
