Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F03%3A00009541" target="_blank" >RIV/00216224:14310/03:00009541 - isvavai.cz</a>
Result on the web
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DOI - Digital Object Identifier
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Alternative languages
Result language
čeština
Original language name
Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
Original language 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.
Czech name
Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers.
Czech description
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Classification
Type
D - Article in proceedings
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Result continuities
Project
<a href="/en/project/LN00A016" target="_blank" >LN00A016: BIOMOLECULAR CENTER</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2003
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Article name in the collection
Materials in Structure Chemistry, Biology, Physics and Technology
ISBN
1211 - 5894
ISSN
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e-ISSN
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Number of pages
1
Pages from-to
23-23
Publisher name
Krystalografická společnost
Place of publication
Praha
Event location
Nové Hrady
Event date
Jan 1, 2003
Type of event by nationality
CST - Celostátní akce
UT code for WoS article
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