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Ingemar André and Sinisa Bjelic (2018) Computational assessment of folding energy landscapes in heterodimeric coiled coils, Proteins: Structure, Function, Bioinformatics,

Wijma, H.J., Floor, R.J., Bjelic S., Marrink, S.J, Baker, D, and Janssen, D.B. (2015) Enantioselective enzymes by computational design and in silico screening, Angewandte Chemie, 127, 3797-801.

Liu, Y., Zhang, X., Tan, Y.L., Bhabha, G., Ekiert, D.C., Kipnis, Y., Bjelic, S., Baker, D., Kelly, J.W. (2014) De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters, Journal of American Chemical Society, 136, 13102-5.

Liu, Y., Tan, Y.L., Zhang, X., Bhabha, G., Ekiert, D.C., Genereux, J.C., Cho, Y.H, Kipnis, Y., Bjelic, S., Baker, D., and Kelly, J.W. (2014) Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts, Proceedings of National Academy of Sciences, 111, 4449-54.

Nivon, L.G., Bjelic, S., King, C., Baker, D. (2014) Automating human intuition for protein design, Proteins: Structure, Function & Bioinformatics, 82, 858-66.

Bjelic, S., Kipnis, Y., Wang, L., Pianowski, Z., Vorobiev, S., Su, M., Seetharaman, J., Xiao, R., Kornhaber, G., Hunt, J.F., Tong, L., Hilvert, D., and Baker, D. (2014) Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design, Journal of Molecular Biology, 426, 256-71.

Bjelic, S., Nivon, L.G., Çelebi-Olçum, N., Kiss, G., Rosewall, C.F., Lovick, H.M., Ingalls, E.L., Gallaher, J.L., Seetharaman, J., Lew, S., Montelione, G.T., Hunt, J.F., Michael, F.E., Houk K.N., and Baker, D. (2013) Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction, ACS Chemical Biology, 8, 749-57.

Richter, F., Leaver-Fay, A., Khare, S.D., Bjelic, S., and Baker, D. (2011) De novo enzyme design using ROSETTA3, PLoS ONE, 6.

Bjelic, S., Brandsdal, B.O., and Åqvist, J. (2008) Cold adaptation of citrate synthase enzyme, Biochmistry 47, 10049-10057.

Bjelic, S., and Åqvist, J. (2006) Catalysis and linear free energy relationships in aspartic proteases, Biochemistry 45, 7709-23.

Bjelic, S., and Åqvist, J. (2004) Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site, Biochemistry 43, 14521-14528.


Åqvist, J., Wennerström, P., Nervall, M., Bjelic, S., and Brandsdal, B.O., (2004) Molecular dynamics simulations of water and biomolecules wit a Monte Carlo constant pressure algorithm, Chemical Physics Letters, 384, 288-294.


Ersmark, K., Feierberg, I., Bjelic, S., Hamelink, E., Hackett, F., Blackman, M.J., Hulten, J., Samuelsson, B., Åqvist, J., and Hallberg, A. (2004) Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity, Journal of Medicinal Chemistry, 47, 110-122.


Ersmark, K., Feierberg, I., Bjelic, S., Hulten, J., Samuelsson, B., Åqvist, J., and Hallberg, A. (2003) C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: Synthesis and theoretical predictions, Bioorganic & Medicinal Chemistry, 11, 3723-3733.



Bjelic, S., Nerval, M., Gutiérrez-de-Terán, H., Ersmark, K., Hallberg, A., and Åqvist, J. (2007) Computational inhibitor design against malaria plasmepsins, CMLS 64, 2285-305.