"0"^^ . "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."@en . "0"^^ . . . . . "617152" . "1"^^ . "2003-01-01+01:00"^^ . "HIV Protease, molecular dynamics"@en . . "[9C205A35AAE0]" . . . . "23-23" . "1"^^ . "K\u0159\u00ED\u017E, Zden\u011Bk" . "Havlas, Zden\u011Bk" . "Krystalografick\u00E1 spole\u010Dnost" . "Materials in Structure Chemistry, Biology, Physics and Technology" . "Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers."@en . . "14310" . "Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers." . "RIV/00216224:14310/03:00009541!RIV/2004/MSM/143104/N" . . "Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers."@cs . . "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." . "P(LN00A016)" . "RIV/00216224:14310/03:00009541" . "Nov\u00E9 Hrady" . "Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers."@en . "Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers." . . "Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers."@cs . . . "Praha" . "Lep\u0161\u00EDk, Martin" . "3"^^ . "1211-5894" . .