291 related articles for article (PubMed ID: 16941468)
1. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.
Thorsteinsdottir HB; Schwede T; Zoete V; Meuwly M
Proteins; 2006 Nov; 65(2):407-23. PubMed ID: 16941468
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases.
Sadiq SK; Wright D; Watson SJ; Zasada SJ; Stoica I; Coveney PV
J Chem Inf Model; 2008 Sep; 48(9):1909-19. PubMed ID: 18710212
[TBL] [Abstract][Full Text] [Related]
4. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.
Zoete V; Michielin O; Karplus M
J Mol Biol; 2002 Jan; 315(1):21-52. PubMed ID: 11771964
[TBL] [Abstract][Full Text] [Related]
5. 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; 52(11):3088-98. PubMed ID: 23121465
[TBL] [Abstract][Full Text] [Related]
6. 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]
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. Computational titration analysis of a multiprotic HIV-1 protease-ligand complex.
Spyrakis F; Fornabaio M; Cozzini P; Mozzarelli A; Abraham DJ; Kellogg GE
J Am Chem Soc; 2004 Sep; 126(38):11764-5. PubMed ID: 15382890
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. 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]
11. Prediction of the binding energy for small molecules, peptides and proteins.
Schapira M; Totrov M; Abagyan R
J Mol Recognit; 1999; 12(3):177-90. PubMed ID: 10398408
[TBL] [Abstract][Full Text] [Related]
12. Structure-based ligand design by dynamically assembling molecular building blocks at binding site.
Liu H; Duan Z; Luo Q; Shi Y
Proteins; 1999 Sep; 36(4):462-70. PubMed ID: 10450088
[TBL] [Abstract][Full Text] [Related]
13. Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor.
Bäckbro K; Löwgren S; Osterlund K; Atepo J; Unge T; Hultén J; Bonham NM; Schaal W; Karlén A; Hallberg A
J Med Chem; 1997 Mar; 40(6):898-902. PubMed ID: 9083478
[TBL] [Abstract][Full Text] [Related]
14. 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]
15. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case.
Meagher KL; Carlson HA
J Am Chem Soc; 2004 Oct; 126(41):13276-81. PubMed ID: 15479081
[TBL] [Abstract][Full Text] [Related]
16. X-ray structure and conformational dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: agreement of time-resolved spectroscopy and molecular dynamics simulations.
Ringhofer S; Kallen J; Dutzler R; Billich A; Visser AJ; Scholz D; Steinhauser O; Schreiber H; Auer M; Kungl AJ
J Mol Biol; 1999 Mar; 286(4):1147-59. PubMed ID: 10047488
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. Nonpeptidal P2 ligands for HIV protease inhibitors: structure-based design, synthesis, and biological evaluation.
Ghosh AK; Kincaid JF; Walters DE; Chen Y; Chaudhuri NC; Thompson WJ; Culberson C; Fitzgerald PM; Lee HY; McKee SP; Munson PM; Duong TT; Darke PL; Zugay JA; Schleif WA; Axel MG; Lin J; Huff JR
J Med Chem; 1996 Aug; 39(17):3278-90. PubMed ID: 8765511
[TBL] [Abstract][Full Text] [Related]
19. Inhibitor binding at the protein interface in crystals of a HIV-1 protease complex.
Brynda J; Rezácová P; Fábry M; Horejsí M; Stouracová R; Soucek M; Hradílek M; Konvalinka J; Sedlácek J
Acta Crystallogr D Biol Crystallogr; 2004 Nov; 60(Pt 11):1943-8. PubMed ID: 15502300
[TBL] [Abstract][Full Text] [Related]
20. 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]
[Next] [New Search]
