Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs)
Apstrakt
Using the crystal structures of inhibitors bound to either group-2 or group-1 neuraminidases (NAs), AScore/ShapeDock (GaDock) scoring was shown to identify the binding modes in agreement with the experiment for all inhibitors docked in their own NA/inhibitor crystal structures. To investigate the effect of small changes in protein structure on predicted binding modes, in a set of 132 docking experiments (11 inhibitors docked in 12 group-2 NA structures), AScore/ShapeDock (GaDock) identified the correct binding modes of 116 complexes. In a total of 88 docking experiments (8 inhibitors docked in 11 group-1 NA structures), AScore/ShapeDock predicted 80 binding modes correctly. Flexible AScore/ShapeDock docking, as quite reproducible, is suggested to be convenient for designing novel H5N1 inhibitors.
Ključne reči:
inhibitors / influenza virus neuraminidase / AScore / ArgusLab 4 / 0Izvor:
Molecular Simulation, 2009, 35, 4, 311-324Izdavač:
- Taylor & Francis Ltd, Abingdon
Finansiranje / projekti:
- Biofizička istraživanja membranskih procesa: interakcija membranskih receptora i kanala sa spoljašnjim faktorima i intracelularna regulacija (RS-MESTD-MPN2006-2010-143016)
DOI: 10.1080/08927020802430752
ISSN: 0892-7022
WoS: 000264134600008
Scopus: 2-s2.0-68149157302
Institucija/grupa
Institut za tehnologiju nuklearnih i drugih mineralnih sirovinaTY - JOUR AU - Mihajlović, Marija AU - Mitrašinović, Petar M. PY - 2009 UR - https://ritnms.itnms.ac.rs/handle/123456789/147 AB - Using the crystal structures of inhibitors bound to either group-2 or group-1 neuraminidases (NAs), AScore/ShapeDock (GaDock) scoring was shown to identify the binding modes in agreement with the experiment for all inhibitors docked in their own NA/inhibitor crystal structures. To investigate the effect of small changes in protein structure on predicted binding modes, in a set of 132 docking experiments (11 inhibitors docked in 12 group-2 NA structures), AScore/ShapeDock (GaDock) identified the correct binding modes of 116 complexes. In a total of 88 docking experiments (8 inhibitors docked in 11 group-1 NA structures), AScore/ShapeDock predicted 80 binding modes correctly. Flexible AScore/ShapeDock docking, as quite reproducible, is suggested to be convenient for designing novel H5N1 inhibitors. PB - Taylor & Francis Ltd, Abingdon T2 - Molecular Simulation T1 - Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs) EP - 324 IS - 4 SP - 311 VL - 35 DO - 10.1080/08927020802430752 UR - conv_556 ER -
@article{ author = "Mihajlović, Marija and Mitrašinović, Petar M.", year = "2009", abstract = "Using the crystal structures of inhibitors bound to either group-2 or group-1 neuraminidases (NAs), AScore/ShapeDock (GaDock) scoring was shown to identify the binding modes in agreement with the experiment for all inhibitors docked in their own NA/inhibitor crystal structures. To investigate the effect of small changes in protein structure on predicted binding modes, in a set of 132 docking experiments (11 inhibitors docked in 12 group-2 NA structures), AScore/ShapeDock (GaDock) identified the correct binding modes of 116 complexes. In a total of 88 docking experiments (8 inhibitors docked in 11 group-1 NA structures), AScore/ShapeDock predicted 80 binding modes correctly. Flexible AScore/ShapeDock docking, as quite reproducible, is suggested to be convenient for designing novel H5N1 inhibitors.", publisher = "Taylor & Francis Ltd, Abingdon", journal = "Molecular Simulation", title = "Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs)", pages = "324-311", number = "4", volume = "35", doi = "10.1080/08927020802430752", url = "conv_556" }
Mihajlović, M.,& Mitrašinović, P. M.. (2009). Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs). in Molecular Simulation Taylor & Francis Ltd, Abingdon., 35(4), 311-324. https://doi.org/10.1080/08927020802430752 conv_556
Mihajlović M, Mitrašinović PM. Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs). in Molecular Simulation. 2009;35(4):311-324. doi:10.1080/08927020802430752 conv_556 .
Mihajlović, Marija, Mitrašinović, Petar M., "Applications of the ArgusLab4/AScore protocol in the structure-based binding affinity prediction of various inhibitors of group-1 and group-2 influenza virus neuraminidases (NAs)" in Molecular Simulation, 35, no. 4 (2009):311-324, https://doi.org/10.1080/08927020802430752 ., conv_556 .