In-house research projects
These projects have evolved as a result of interactions with glycobiologists in academic groups, mainly at Sahlgren's academy, Göteborg University. We have been working on docking the Norovirus surface protein with natural carbohydrate ligands as a prelude to structure base design of adhesion inhibitors. In these projects we have been doing the modelling while our collaborators have done the wet lab tests. Part of that work has been directed against the design of a treatment for winter-vomiting disease.
Furthermore, we support industrial PhD projects (ref. 1-5). Currently having such a project concerning protein-ligand docking.
Publications:
[1] Strino F, Lii JH, Koppisetty CAK, Nyholm PG, Gabius HJ, 2010. Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity. J Comput Aided Mol Des. 24:1009-21.
[2] Koppisetty C.A.K., Nasir W., Strino F., Rydell G.E., Larson G., Nyholm P.-G., 2010. Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data. J Comput Aided Mol Des 24:423–431
[3] Strino, F.; Lii, H.-J.; Gabius, H.-J.; Nyholm, P.-G., 2009, Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4. Implications for design of non-hydrolysable mimetics. J Aided Mol Des, 23: 845-52.
[4] Strino, F.; Nahmany, A.; Rosen, J.; Kemp, G. J. L.; Sá-correia, I.; Nyholm, P.-G., 2005, Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search. Carbohydr Res 340,(5), 1019-24.
[5] Nahmany, A.; Strino, F.; Rosen, J.; Kemp, G. J. L.; Nyholm, P.-G., 2005, The use of a genetic algorithm search for molecular mechanics(MM3)-based conformational analysis of oligosaccharides. Carbohydr Res 340, (5), 1059-64.