2003
Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
LEPŠÍK, Martin, Zdeněk KŘÍŽ a Zdeněk HAVLASZákladní údaje
Originální název
Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
Název anglicky
Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
Autoři
LEPŠÍK, Martin (203 Česká republika), Zdeněk KŘÍŽ (203 Česká republika, garant) a Zdeněk HAVLAS (203 Česká republika)
Vydání
Praha, Materials in Structure Chemistry, Biology, Physics and Technology, od s. 23-23, 1 s. 2003
Nakladatel
Krystalografická společnost
Další údaje
Jazyk
čeština
Typ výsledku
Stať ve sborníku
Obor
10403 Physical chemistry
Stát vydavatele
Česká republika
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Kód RIV
RIV/00216224:14310/03:00009541
Organizační jednotka
Přírodovědecká fakulta
ISBN
1211 - 5894
Klíčová slova anglicky
HIV Protease; molecular dynamics
Štítky
Změněno: 17. 3. 2004 15:39, Mgr. Zdeněk Kříž, Ph.D.
V originále
The inhibitory potency of four nanomolar diastereomeric inhibitors of HIV-1 protease [1] was studied by molecular dynamics simulations and MM-GBSA/PBSA analysis. As a starting point we used the crystal structures of protease-inhibitor complexes [2, 3]. Having added hydrogens, we surrounded the complexes with a box of explicit water molecules and added counterions to neutralize the box. Using AMBER 7 program package [4], we minimized, heated and equilibrated the system after which we ran 2-nanosecond-long production dynamics. Periodic boundary conditions were used and long-range electrostatics was treated by particle mesh Ewald (PME) technique. An analysis of the molecular dynamical trajectories was performed and their quality assessed. The protease-inhibitor binding energies were calculated with MM-GBSA/PBSA approach. The effect of the length of the simulation, method to calculate solvation energy, and other factors upon the results was determined.
Anglicky
The inhibitory potency of four nanomolar diastereomeric inhibitors of HIV-1 protease [1] was studied by molecular dynamics simulations and MM-GBSA/PBSA analysis. As a starting point we used the crystal structures of protease-inhibitor complexes [2, 3]. Having added hydrogens, we surrounded the complexes with a box of explicit water molecules and added counterions to neutralize the box. Using AMBER 7 program package [4], we minimized, heated and equilibrated the system after which we ran 2-nanosecond-long production dynamics. Periodic boundary conditions were used and long-range electrostatics was treated by particle mesh Ewald (PME) technique. An analysis of the molecular dynamical trajectories was performed and their quality assessed. The protease-inhibitor binding energies were calculated with MM-GBSA/PBSA approach. The effect of the length of the simulation, method to calculate solvation energy, and other factors upon the results was determined.
Návaznosti
| LN00A016, projekt VaV |
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