Primary Citation PubMed: 11170214
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Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.
(2011) PLoS One 6
PubMed: 21738569 | PubMedCentral: PMC3126794 | DOI: 10.1371/journal.pone.0019830
 (PDB ID 1G6L) and the solution structure of PR monomer reported by Ishima et al.
Publication Year: 2011
Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex.
(2012) PLoS One 7
PubMed: 22457784 | PubMedCentral: PMC3311648 | DOI: 10.1371/journal.pone.0033709
In fact, selecting 1rd8, 2hu4, 1nyj, 3cm8, 3hw3, 1g6l, 2jle, 2gv9, 3gbn, 3gbm, 3fku, 3sdy, 3ztn and 3ztj as the target proteins, and choosing Amantadine, Aspirin, Azithromycin, HEM, Heroin, Isosorbide... Oseltamivir, Zanamivir and Vancomycin as the panel of drugs, then all of these ligands are predicted to be docked with the same pocket on each of above target proteins if these ligands can be packed into this pocket, while all of those ligands will arrive at the minimal value of minimal free energy at a neighborhood of the pocket if those ligands can not be packed into this pocket.
Publication Year: 2012
Mining the protein data bank to differentiate error from structural variation in clustered static structures: an examination of HIV protease.
(2012) Viruses 4
PubMed: 22590675 | PubMedCentral: PMC3347031 | DOI: 10.3390/v4030348
Several exhibited the closed flap conformation, though closer examination revealed these to belong to covalently-bonded PR dimers (PDB IDs 1g6l and 1lv1) that were split into monomers by removing the ... ridge of connecting residues.
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