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Description
| - 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.
- 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)
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Title
| - 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. (en)
- Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers. (cs)
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skos:prefLabel
| - 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. (en)
- Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers. (cs)
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skos:notation
| - RIV/00216224:14310/03:00009541!RIV/2004/MSM/143104/N
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http://linked.open.../vavai/riv/strany
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http://linked.open...avai/riv/aktivita
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http://linked.open...avai/riv/aktivity
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http://linked.open...vai/riv/dodaniDat
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http://linked.open...aciTvurceVysledku
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http://linked.open.../riv/druhVysledku
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http://linked.open...iv/duvernostUdaju
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http://linked.open...titaPredkladatele
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http://linked.open...dnocenehoVysledku
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http://linked.open...ai/riv/idVysledku
| - RIV/00216224:14310/03:00009541
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http://linked.open...riv/jazykVysledku
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http://linked.open.../riv/klicovaSlova
| - HIV Protease, molecular dynamics (en)
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http://linked.open.../riv/klicoveSlovo
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http://linked.open...ontrolniKodProRIV
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http://linked.open...v/mistoKonaniAkce
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http://linked.open...i/riv/mistoVydani
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http://linked.open...i/riv/nazevZdroje
| - Materials in Structure Chemistry, Biology, Physics and Technology
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http://linked.open...in/vavai/riv/obor
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http://linked.open...ichTvurcuVysledku
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http://linked.open...cetTvurcuVysledku
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http://linked.open...ocetUcastnikuAkce
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http://linked.open...nichUcastnikuAkce
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http://linked.open...vavai/riv/projekt
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http://linked.open...UplatneniVysledku
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http://linked.open...iv/tvurceVysledku
| - Lepšík, Martin
- Kříž, Zdeněk
- Havlas, Zdeněk
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http://linked.open...vavai/riv/typAkce
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http://linked.open.../riv/zahajeniAkce
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issn
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number of pages
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http://purl.org/ne...btex#hasPublisher
| - Krystalografická společnost
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http://localhost/t...ganizacniJednotka
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