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Results: 1 to 20 of 207

1.

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 24;50(5):890-905. doi: 10.1021/ci100007w.

PMID:
20384328
[PubMed - indexed for MEDLINE]
2.

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations.

Hu GD, Zhu T, Zhang SL, Wang D, Zhang QG.

Eur J Med Chem. 2010 Jan;45(1):227-35. doi: 10.1016/j.ejmech.2009.09.048. Epub 2009 Oct 13.

PMID:
19910081
[PubMed - indexed for MEDLINE]
3.

A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: a systematic MM-PBSA and thermodynamic integration study.

Leonis G, Steinbrecher T, Papadopoulos MG.

J Chem Inf Model. 2013 Aug 26;53(8):2141-53. doi: 10.1021/ci4002102. Epub 2013 Jul 24.

PMID:
23834142
[PubMed - indexed for MEDLINE]
4.

Structural analysis of an HIV-1 protease I47A mutant resistant to the protease inhibitor lopinavir.

Kagan RM, Shenderovich MD, Heseltine PN, Ramnarayan K.

Protein Sci. 2005 Jul;14(7):1870-8. Epub 2005 Jun 3.

PMID:
15937277
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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. doi: 10.1021/ci8000937. Epub 2008 Aug 19.

PMID:
18710212
[PubMed - indexed for MEDLINE]
6.

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 1;57(2):279-93.

PMID:
15340915
[PubMed - indexed for MEDLINE]
7.

Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant.

Todd MJ, Luque I, Velázquez-Campoy A, Freire E.

Biochemistry. 2000 Oct 3;39(39):11876-83.

PMID:
11009599
[PubMed - indexed for MEDLINE]
8.

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 27;130(8):2639-48. doi: 10.1021/ja0779250. Epub 2008 Jan 29.

PMID:
18225901
[PubMed - indexed for MEDLINE]
9.

Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes.

Velazquez-Campoy A, Vega S, Freire E.

Biochemistry. 2002 Jul 9;41(27):8613-9.

PMID:
12093278
[PubMed - indexed for MEDLINE]
10.

Resolution of discordant HIV-1 protease resistance rankings using molecular dynamics simulations.

Wright DW, Coveney PV.

J Chem Inf Model. 2011 Oct 24;51(10):2636-49. doi: 10.1021/ci200308r. Epub 2011 Oct 7.

PMID:
21902276
[PubMed - indexed for MEDLINE]
11.

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. doi: 10.1021/ci900012k.

PMID:
19537723
[PubMed - indexed for MEDLINE]
12.

Multidrug resistance to HIV-1 protease inhibition requires cooperative coupling between distal mutations.

Ohtaka H, Schön A, Freire E.

Biochemistry. 2003 Nov 25;42(46):13659-66.

PMID:
14622012
[PubMed - indexed for MEDLINE]
13.

Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach.

Jenwitheesuk E, Samudrala R.

Antivir Ther. 2005;10(1):157-66.

PMID:
15751773
[PubMed - indexed for MEDLINE]
14.

A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease.

Vega S, Kang LW, Velazquez-Campoy A, Kiso Y, Amzel LM, Freire E.

Proteins. 2004 May 15;55(3):594-602.

PMID:
15103623
[PubMed - indexed for MEDLINE]
16.

Structural and thermodynamic basis of resistance to HIV-1 protease inhibition: implications for inhibitor design.

Velazquez-Campoy A, Muzammil S, Ohtaka H, Schön A, Vega S, Freire E.

Curr Drug Targets Infect Disord. 2003 Dec;3(4):311-28. Review.

PMID:
14754432
[PubMed - indexed for MEDLINE]
17.

Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies.

Meher BR, Wang Y.

J Phys Chem B. 2012 Feb 16;116(6):1884-900. doi: 10.1021/jp2074804. Epub 2012 Feb 3.

PMID:
22239286
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.

Muzammil S, Armstrong AA, Kang LW, Jakalian A, Bonneau PR, Schmelmer V, Amzel LM, Freire E.

J Virol. 2007 May;81(10):5144-54. Epub 2007 Mar 14.

PMID:
17360759
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.

Hansson T, Aqvist J.

Protein Eng. 1995 Nov;8(11):1137-44.

PMID:
8819979
[PubMed - indexed for MEDLINE]
20.

Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity.

Logsdon BC, Vickrey JF, Martin P, Proteasa G, Koepke JI, Terlecky SR, Wawrzak Z, Winters MA, Merigan TC, Kovari LC.

J Virol. 2004 Mar;78(6):3123-32.

PMID:
14990731
[PubMed - indexed for MEDLINE]
Free PMC Article

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