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Results: 1 to 20 of 48

1.

New insights into the in silico prediction of HIV protease resistance to nelfinavir.

Antunes DA, Rigo MM, Sinigaglia M, de Medeiros RM, Junqueira DM, Almeida SE, Vieira GF.

PLoS One. 2014 Jan 31;9(1):e87520. doi: 10.1371/journal.pone.0087520. eCollection 2014.

PMID:
24498124
[PubMed - in process]
Free PMC Article
2.

Whiskers-less HIV-protease: a possible way for HIV-1 deactivation.

Dayer MR, Dayer MS.

J Biomed Sci. 2013 Sep 12;20:67. doi: 10.1186/1423-0127-20-67.

PMID:
24024748
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations.

Xia J, Deng NJ, Levy RM.

J Phys Chem B. 2013 Jun 6;117(22):6625-34. doi: 10.1021/jp400797y. Epub 2013 May 28.

PMID:
23638941
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease.

de Vera IM, Smith AN, Dancel MC, Huang X, Dunn BM, Fanucci GE.

Biochemistry. 2013 May 14;52(19):3278-88. doi: 10.1021/bi400109d. Epub 2013 May 1.

PMID:
23566104
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Small molecule regulation of protein conformation by binding in the Flap of HIV protease.

Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD.

ACS Chem Biol. 2013;8(6):1223-31. doi: 10.1021/cb300611p. Epub 2013 Mar 29.

PMID:
23540839
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Inhibitor-induced conformational shifts and ligand-exchange dynamics for HIV-1 protease measured by pulsed EPR and NMR spectroscopy.

Huang X, de Vera IM, Veloro AM, Blackburn ME, Kear JL, Carter JD, Rocca JR, Simmerling C, Dunn BM, Fanucci GE.

J Phys Chem B. 2012 Dec 13;116(49):14235-44. doi: 10.1021/jp308207h. Epub 2012 Nov 30.

PMID:
23167829
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation.

Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA.

J Chem Theory Comput. 2012 Oct 9;8(10):3452-3462. Epub 2012 Apr 17.

PMID:
23144597
[PubMed]
Free PMC Article
8.

Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.

Humphris-Narayanan E, Akiva E, Varela R, Ó Conchúir S, Kortemme T.

PLoS Comput Biol. 2012;8(8):e1002639. doi: 10.1371/journal.pcbi.1002639. Epub 2012 Aug 23.

PMID:
22927804
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Molecular dynamics simulation in virus research.

Ode H, Nakashima M, Kitamura S, Sugiura W, Sato H.

Front Microbiol. 2012 Jul 19;3:258. doi: 10.3389/fmicb.2012.00258. eCollection 2012.

PMID:
22833741
[PubMed]
Free PMC Article
10.

Temperature-sensitive mutants and revertants in the coronavirus nonstructural protein 5 protease (3CLpro) define residues involved in long-distance communication and regulation of protease activity.

Stobart CC, Lee AS, Lu X, Denison MR.

J Virol. 2012 May;86(9):4801-10. doi: 10.1128/JVI.06754-11. Epub 2012 Feb 15.

PMID:
22345451
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease.

Mittal S, Cai Y, Nalam MN, Bolon DN, Schiffer CA.

J Am Chem Soc. 2012 Mar 7;134(9):4163-8. doi: 10.1021/ja2095766. Epub 2012 Feb 28.

PMID:
22295904
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

Torbeev VY, Raghuraman H, Hamelberg D, Tonelli M, Westler WM, Perozo E, Kent SB.

Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):20982-7. doi: 10.1073/pnas.1111202108. Epub 2011 Dec 8.

PMID:
22158985
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

HIV-1 Protease: Structural Perspectives on Drug Resistance.

Weber IT, Agniswamy J.

Viruses. 2009 Dec;1(3):1110-36. doi: 10.3390/v1031110. Epub 2009 Dec 3.

PMID:
21994585
[PubMed]
Free PMC Article
15.

Fragment screening and HIV therapeutics.

Bauman JD, Patel D, Arnold E.

Top Curr Chem. 2012;317:181-200. doi: 10.1007/128_2011_232. Review.

PMID:
21972022
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Dynamical basis for drug resistance of HIV-1 protease.

Mao Y.

BMC Struct Biol. 2011 Jul 8;11:31. doi: 10.1186/1472-6807-11-31.

PMID:
21740562
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.

Borkar AN, Rout MK, Hosur RV.

PLoS One. 2011;6(6):e19830. doi: 10.1371/journal.pone.0019830. Epub 2011 Jun 29.

PMID:
21738569
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Molecular recognition in the case of flexible targets.

Ivetac A, McCammon JA.

Curr Pharm Des. 2011;17(17):1663-71.

PMID:
21619526
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Binding to the open conformation of HIV-1 protease.

Lexa KW, Carlson HA.

Proteins. 2011 Jul;79(7):2282-90. doi: 10.1002/prot.23054. Epub 2011 May 20.

PMID:
21604303
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

Deng NJ, Zheng W, Gallicchio E, Levy RM.

J Am Chem Soc. 2011 Jun 22;133(24):9387-94. doi: 10.1021/ja2008032. Epub 2011 May 25.

PMID:
21561098
[PubMed - indexed for MEDLINE]
Free PMC Article

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