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-based 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.
We have supported several PhD projects regarding conformational analyses of carbohydrates and protein-ligand docking (ref. 1-11).
 Reithmeier A, Lundbäck T, Haraldsson M, Frank M, Ek-Rylander B, Nyholm PG, Gustavsson AL, Andersson G. 2018 Identification of inhibitors of Tartrate-resistant acid phosphatase (TRAP/ACP5) activity by small-molecule screening. Chem Biol Drug Des., 92,1255-1271
 Nasir W, Frank b, Kunze A, Bally M, Parra M, Nyholm P-G, Höök F, Larson G. 2017, Histo-blood group antigen presentation is critical for norovirus VLP binding to glycosphingolipids in model membranes. ACS Chemical Biology, 12,1288-1296
 Koppisetty CA, Frank M, Lyubartsev AP, Nyholm PG 2015, Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations..J Comput Aided Mol Des.29(1):13-21.
 Krumpel M, Reithmeier A, Senge T, Baeumler TA, Frank M, Nyholm PG, Ek-Rylander B, Andersson G. 2015 The small chemical enzyme inhibitor 5-phenylnicotinic acid/CD13 inhibits cell migration and invasion of tartrate-resistant acid phosphatase/ACP5-overexpressing MDA-MB-231 breast cancer cells. Exp Cell Res.,339(1):154-62.
 Koppisetty CA, Frank M, Kemp GJ, Nyholm PG, 2013. Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein-Ligand Complexes Using Support Vector Machines. J Chem Inf Model; 53:2559-70
 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.
 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
 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 Comput Aided Mol Des, 23: 845-52.
 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.
 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.