Protein-glycosaminoglycan interactions: computational approaches


1. Drobot B., Schmidt M., Mochizuki Y., Abe T., Okuwaki K., Brulfert F., Falke S., Samsonov S. A., Komeiji Y., Betzel C., Stumpf T., Raff J., Tsushima S. Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin. Phys Chem Chem Phys. 2019, Vol. 21: 21213-21222.

2. Bojarski K. K., Becher J., Riemer T., Lemmnitzer K., Moeller S., Schiller J., Schnabelrauch M., Samsonov S.A. Synthesis and in silico characterization of artificially phosphorylated glycosaminoglycans. J Mol Struct. 2019, Vol. 1197:401-416.

3. Samsonov S. A., Feza S., Zsila F. In silico analysis of heparin and chondroitin sulfate binding mechanisms of the antiprotozoal drug berenil and pentamidine. Carb Res. 2019, 482:107742.

4. Penk A., Baumann L., Huster D., Samsonov S. A. NMR and Molecular Modeling Reveal Specificity of the Interactions between CXCL14 and Glycosaminoglycans. Glycobiology, 2019, Vol. 29: 715-725.

5. Kohut G., Sieradzan A., Zsila F., Tunde J., Bosze S., Liwo A., Samsonov S. A., Beke-Somfai T. The Molecular Mechanism of Structural Changes in the Antimicrobial Peptide CM15 Upon Complex Formation with Drug Molecule Suramin: a Computational Analysis. Phys Chem Chem Phys. 2019, Vol.21: 10644-10659.

6. Uciechowska-Kaczmarzyk U., Chauvot de Beauchene I., Samsonov S. A. Docking software performance in protein-glycosaminoglycan systems. J Mol Graph Mod. 2019, Vol. 90:42-50.

7. Samsonov S. A., Zacharias M., Chauvot de Beauchene I. Modeling large protein-glycosaminoglycan complexes using a fragment-based approach. J Comp Chem. 2019, Vol. 40:1429-1439.

8. Samsonov S. A., Lubecka E. A., Bojarski K. K. , Ganzynkowicz R., Liwo A. Local and Long Range Potentials for Heparin-Protein Systems for Coarse-Grained Simulations. Biopolymers. 2019, Vol. 110:e23269.

9. Bojarski K. K., Sieradzan A.K.,Samsonov S. A., Molecular Dynamics Insights into Protein-Glycosaminoglycan Systems from Microsecond-Scale Simulations. Biopolymers. 2019, Vol. 110:e23252.


1. Kohut G., Liwo A., Bosze S., Beke-Somfai T., Samsonov S. A. Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges for Flexible Systems. J Phys Chem B. 2018. Vol. 122:7821-7827.

2. Vallet S.D., Miele A.E., Uciechowska-Kaczmarzyk U., Liwo A., Duclos B., Samsonov S. A. , Ricard-Blum S. Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners. Sci Rep. 2018. Vol. 8:11768.

3. Uciechowska-Kaczmarzyk U., Babik S., Zsila F., Bojarski K.K., Beke-Somfai T., Samsonov S. A. Molecular Dynamics-Based Model of VEGF-A and Its Heparin Interactions. J Mol Graph Mod. 2018. Vol 82:157-166.

4. Zsila F., Samsonov S. A., Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis. Carbohydarate Research. 2018. 462:28-33.

5. Samsonov S. A. Computational analysis of solvent inclusion in docking studies of protein-glycosaminoglycan systems. Computational Drug Discovery and Design. Methods in Molecular Biology Series. Springer. 2018, Vol 1762:445-454.

6. Nordsieck K., Baumann L., Hintze V., Pisabarro M. T., Schnabelrauch M., Beck-Sickenger A. G., Samsonov S. A. The effect of interleukin-8 truncations on its interactions with glycosaminoglycans. Biopolymers. 2018. 109(10):e23103.

7. Bojarski K. K., Samsonov S. A. Glycosaminoglycans mediate the function of cathepsin proteases. Review. ‘VII All Polish Conference: Young Scientists in Poland – Research and Development’. Wydawnictwo Młodzi Naukowcy ,2018. [PDF]

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665778.