caa a22 4500 605510946 CHVBK 20210128100648.0 cr unu---uuuuu 210128e20150601xx s 000 0 eng 10.1007/s00894-015-2713-2 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2713-2 Comparative evaluation of several docking tools for docking small molecule ligands to DC-SIGN [Elektronische Daten] [Gregor Jug, Marko Anderluh, Tihomir Tomašič] Five docking tools, namely AutoDock, FRED, CDOCKER, FlexX and GOLD, have been critically examined, with the aim of selecting those most appropriate for use as docking tools for docking molecules to the lectin dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN). This lectin has been selected for its rather non-druggable binding site, which enables complex interactions that guide the binding of the core monosaccharide. Since optimal orientation is crucial for forming coordination bonds, it was important to assess whether the selected docking tools could reproduce the optimal binding conformation for several oligosaccharides that are known to bind DC-SIGN. Our results show that even widely used docking programs have certain limitations when faced with a rather shallow and featureless binding site, as is the case of DC-SIGN. The FRED docking software (OpenEye Scientific Software, Inc.) was found to score as the best tool for docking ligands to DC-SIGN. The performance of FRED was further assessed on another lectin, Langerin. We have demonstrated that this validated docking protocol could be used for docking to other lectins similar to DC-SIGN. Springer-Verlag Berlin Heidelberg, 2015 Antagonists nationallicence Anti-infectives nationallicence DC-SIGN nationallicence Docking nationallicence Docking validation nationallicence HIV-1 nationallicence Jug Gregor Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia aut Anderluh Marko Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia aut Tomašič Tihomir Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/6(2015-06-01), 1-12 1610-2940 21:6<1 2015 21 894 https://doi.org/10.1007/s00894-015-2713-2 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2713-2 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Jug Gregor Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia aut NATIONALLICENCE 700 1- Anderluh Marko Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia aut NATIONALLICENCE 700 1- Tomašič Tihomir Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/6(2015-06-01), 1-12 1610-2940 21:6<1 2015 21 894