Giatagana E-M., Berdiaki A., Gaardløs M., Tsatsakis A., Samsonov S.A., Nikitovic D. Rapamycin- induced autophagy in osteosarcoma cells is mediated via the biglycan/Wnt/β-catenin signaling axis American Journal of Physiology-Cell Physiology. 2022. Epub.

Kogut M.M., Grabowska O., Wyrzykowski D., Samsonov S.A. Affinity and putative entrance mechanisms of alkyl sulfates into the β-CD cavity Journal of Molecular Liquids. 2022. Vol. 364: 119978.

Kogut M.M.Danielsson A., Ricard-Blum S., Samsonov S.A. Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis Computational Biology and Chemistry. 2022. Vol. 99: 107727.

Marcisz M., Gaardløs M.Bojarski K.K., Siebenmorgen T., Zacharias M., Samsonov S.A. Explicit Solvent Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) in Molecular Modeling of Protein-Glycosaminoglycan Complexes J Comp Chem. 2022. Vol. 43: 1633–1640.

Danielsson A.Kogut M.M.Maszota-Zieleniak M., Chopra P., Boons G.J., Samsonov S.A. Molecular Dynamics-based descriptors of 3-O-Sulfated Heparan Sulfate as Contributors of Protein Binding Specificity Computational Biology and Chemistry. 2022. Vol. 99: 107716.

Denamur S., Chazeirat T., Masztoa-Zieleniak M., Vives R., Saidi A., Zhang F., Linhardt R.J., Labarthe F., Samsonov S.A., Lalmanach G., Lecaille F. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L:consequences in mucopolysaccharidosis Carbohydrate Polymers. 2022. Vol. 293: 119734.

Lipska A.G., Anoniak A. M., Wesolowski P., Warszawski A., Samsonov S.A., Sieradzan A.K. Coarse- grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins Journal of Molecular Modeling. 2022. Vol. 293: 119734.

Bertozo L., Kogut M., Maszota-Zieleniak A.Samsonov S.A., Ximenez V.F. Induced Circular Dichroism as a Tool to Monitor the Displacement of Ligands Between Albumins Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2022. Vol. 278: 121374.

Maszota-Zieleniak M., Zsila F., Samsonov S.A. Molecular Dynamics Approaches Dissect Molecular Mechanisms Underlying Methylene Blue–Glycosaminoglycan Interactions Molecules. 2022. Vol. 27: 2654.

Giatagana E-M., Berdiaki A., Gaardløs M.Samsonov S.A., Tzanakakis G.N., Nikitovic D. Biglycan interacts with type I insulin-like receptor (IGF-IR) signaling pathway to regulate osteosarcoma progression and response to chemotherapy Cancers. 2022. Vol 14: 1196.

Bojarski K.K., Sage J., Lalmanach G., Lecaille F., Samsonov S.A. In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V J Mol Graph Mod. 2022. Vol. 113: 108153

Sage J., Renault J., Domain R., Bojarski K.K., Chazeirat T., Saidi A., Leblanc E., Nizard C., Samsonov S.A., Kurfurst R., Lalmanach G., Lecaille F. Modulation of the expression and activity of cathepsin S in reconstructed human skin by neohesperidin dihydrochalcone Matrix Biology. 2022. Vol. 107: 97-112

Kogut M.M.Marcisz M.Samsonov S.A. Modeling glycosaminoglycan-protein complexes Current Opinion in Structural Biology. 2022.

Liwo A., Sieradzan A.K., Karczyńska A.S., Lubecka E.A., Samsonov S.A., Czaplewski C., Krupa P., Mozolewska M. Practical Aspects of Computational Chemistry V. Chapter: Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry Springer Nature Switzerland AG. 2022.

Grabowska O., Kogut M.M., Żamojć K., Samsonov S.A., Makowska J., Tesmar A., Chmur K., Wyrzykowski D., Chmurzyński L. Effect of Tetraphenylborate on Physicochemical Properties of Bovine Serum Albumin Molecules. 2021. Vol. 26: 6565

Marcisz M.Maszota-Zieleniak M., Huard B., Samsonov S.A. Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans Biomolecules. 2021. Vol. 11: 1349.

Liwo A., Czaplewski C., Sieradzan A.K., Lipska A.G., Samsonov S.A., Murarka R.K. Theory and practice of coarse-grained molecular dynamics Biomolecules. 2021. Vol. 11: 1347.

Lensink M.F., Brysbaert G., Mauri T., Nadzirin N., Velankar S., Chaleil R.A.G., Clarence T., Bates P.A., Kong R., Liu B., Yang G., Liu M., Shi H., Lu X., Chang S., Roy R.S., Quadir F., Liu J., Cheng J., Antoniak A., Czaplewski C., Giełdoń A., Kogut M., Lipska A.G., Liwo A., Lubecka E.A., Maszota-Zieleniak M., Sieradzan A.K., Ślusarz R., Wesołowski P.A., Zięba K., De Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment Proteins. 2021.

Marcisz M., Zacharias M., Samsonov S.A. Modeling protein-glycosaminoglycan complexes: does the size matter? J Chem Inf Mod. 2021. Vol. 61: 4475–4485.

Antoniak A., Biskupek I., Bojarski K.K., Czaplewski C., Giełdoń A.,Kogut M., Kogut M.M., Krupa P., Lipska A.G., Liwo A., Lubecka E.A., Marcisz M.Maszota-Zieleniak M.Samsonov S.A., Sieradzan A.K., Ślusarz M.J., Ślusarz R., Wesołowski P.A., Ziȩba K. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment J Mol Graph Mod. 2021. 108:108008

Tesmar A., Kogut M.M., Żamojć K., Grabowska O., Chmur K., Samsonov S.A., Makowska J., Wyrzykowski D., Chmurzyński L. Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches Journal of Molecular Liquids. 2021. Vol. 340: 117185

Maszota-Zieleniak M.Danielsson A.Samsonov S.A. The potential role of glycosaminoglycans in serum amyloid A fibril formation by in silico approaches Matrix Biology Plus. 2021. Vol. 12: 100008

Maszota-Zieleniak M., Zsila F., Samsonov S.A. Computational insights into heparin-small molecule interactions: evaluation of the balance between stacking and non-stacking binding modes. Carbohydrate Research Carbohydrate Research. 2021. Vol. 507: 108390

Künze G., Huster D., Samsonov S.A. Investigation of the Structure of Regulatory Proteins Interacting with Glycosaminoglycans by Combining NMR Spectroscopy and Molecular Modeling – The Beginning of a Wonderful Friendship Biological Chemistry. 2021.

Gaardløs M., Samsonov S.A. , Sletmoen M., Sætrom G.I., Hjørnevik M., Sletta H., Tøndervik A., Aachmann F.L. Insights into the roles of charged residues in binding and processivity of mannuronan C-5 epimerase AlgE4 Glycobiology. 2021.

Marcisz M., Huard B., Lipska A.G., Samsonov S.A. Further analyses of APRIL/APRIL- Receptor/Glycosaminoglycan interactions by biochemical assays linked to computational studies Glycobiology. 2021.

Bertozo L. C., Maszota-Zieleniak M., Bolean M., Ciancaglini P., Samsonov S.A., Ximenes V.F. Binding of fluorescent dansyl amino acids in albumin: when the access to the protein cavity is more important than the strength of binding Dyes and Pigments. 2021. Vol. 188: 109195

Maszota-Zieleniak M.Marcisz M.Kogut M.M., Siebenmorgen T., Zacharias M., Samsonov S.A. Evaluation of Replica Exchange with Repulsive Scaling Approach for Docking Glycosaminoglycans J Comp Chem. 2021. Vol. 42: 1040–1053

Samsonov S.A., Zsila F., Maszota-Zieleniak M. Acute phase α1-acid glycoprotein as a siderophore-capturing component of the human plasma: a molecular modeling study J Mol Graph Mod. 2021. 105:107861

Kogut M.M.Maszota-Zieleniak M.Marcisz M.Samsonov S.A. Computational insights into the calcium ions role in protein-glycosaminoglycan systems. Phys Chem Chem Phys. 2021. Vol. 23: 3519–3530.

Bojarski K.K.Samsonov S.A. Role of oligosaccharide chain polarity in protein-glycosaminoglycan interactions. J Chem Inf Mod. 2021. Vol. 61: 455–466.

Zsila F., Samsonov S.A.Maszota-Zieleniak M. Mind your dye: the amyloid sensor thioflavin T interacts with sulfated glycosaminoglycans used to induce cross-β-sheet motifs. J Phys Chem B. 2020. Vol. 124: 11625–11633.

Chazeirat T., Denamur S., Bojarski K.K., Andrault P.M., Sizaret D., Zhang F., Saidi A., Tardieu M., Linhardt R.J., Labarthe F., Brömme D., Samsonov S.A., Lalmanach G., Lecaille F. The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V. Carbohydrate Polymers. 2020. Vol. 253:117261.

Gorbikova E., Samsonov S.A., Kalendar R. Probing proton-loading site of cytochrome c oxidase by time-resolved Fourier transform infrared spectroscopy. Molecules. 2020. Vol. 25:3393.

Bojarski K.K., Karczyńska A.S., Samsonov S.A. The role of glycosaminoglycans in procathepsin B maturation – molecular mechanism elucidated by a computational study. J Chem Inf Mod. 2020. Vol. 60:2247–2256.

Gitlin-Domagalska A., Dębowski D., Gucwa K., Starego D., Ptaszyńska N., Sieradzan A., Karczyńska A., Samsonov S.A., Mangold M., Gütschow M., Łęgowska A., Rolka K. Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability. Biochemie. Vol. 171–172:178–186.

Karczyńska A., Zięba K., Uciechowska U., Mozolewska, M., Krupa P., Lubecka E., Lipska A., Sikorska C., Samsonov S., Sieradzan A., Gieldon A., Liwo A., Ślusarz R., Ślusarz M., Lee, J., Joo K., Czaplewski C. Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13. J Chem Inf Mod. 2020. Vol. 60:1844–1864.

Glashagen G., de Vries S., Uciechowska-Kaczmarzyk U.Samsonov S.A., Murail S., Tuffery P., Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins. 2019. Vol. 88:1018–1028.

Lecaille F., Chazeirat T., Bojarski K.K., Renault J., Saidi A., Prasad V.G.N.V, Samsonov S.A., Lalmanach G. Rat cathepsin K: enzymatic specificity and regulation of its collagenolytic activity. BBA – Proteins and Proteomics. 2019, Vol. 1868:140318.

Plotnikova M.A., Klotchenko S.A., Kiselev A.A., Gorshkov A.N., Shurygina A.S., Vasilyev K.A., Uciechowska-Kaczmarzyk U.Samsonov S.A., Kovalenko A.L., Vasin A.V. Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway. Sci Rep. 2019, Vol. 9:18240.

Lensink M.F., Brysbaert G., Nadzirin N., Velankar S., Chaleil R.A.G., Gerguri T., Bates P.A., Laine E., Carbone A., Grudinin S., Kong R., Liu R.R., Xu X.M., Shi H., Chang S., Eisenstein M., Karczynska A., Czaplewski C., Lubecka E., Lipska A., Krupa P., Mozolewska M., Golon Ł., Samsonov S., Liwo A., Crivelli S., Pagès G., Karasikov M., Kadukova M., Yan Y., Huang S.Y., Rosell M., Rodríguez-Lumbreras L.A., Romero-Durana M., Díaz-Bueno L., Fernandez-Recio J., Christoffer C., Terashi G., Shin W.H., Aderinwale T., Maddhuri Venkata Subraman S.R., Kihara D., Kozakov D., Vajda S., Porter K., Padhorny D., Desta I., Beglov D., Ignatov M., Kotelnikov S., Moal I.H., Ritchie D.W., Chauvot de Beauchêne I., Maigret B., Devignes M.D., Ruiz Echartea M.E., Barradas-Bautista D., Cao Z., Cavallo L., Oliva R., Cao Y., Shen Y., Baek M., Park T., Woo H., Seok C., Braitbard M., Bitton L., Scheidman-Duhovny D., Dapkūnas J., Olechnovič K., Venclovas Č., Kundrotas P.J., Belkin S., Chakravarty D., Badal V.D., Vakser I.A., Vreven T., Vangaveti S., Borrman T., Weng Z., Guest J.D., Gowthaman R., Pierce B.G., Xu X., Duan R., Qiu L., Hou J., Ryan Merideth B., Ma Z., Cheng J., Zou X., Koukos P.I., Roel-Touris J., Ambrosetti F., Geng C., Schaarschmidt J., Trellet M.E., Melquiond A.S.J., Xue L., Jiménez-García B., van Noort C.W., Honorato R.V., Bonvin A.M.J.J., Wodak S.J. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins. 2019, Vol. 87:1200–1221.

Potthoff J.Bojarski K.K., Kohut G., Lipska A.G., Liwo A., Kessler E., Ricard-Blum S., Samsonov S.A. Analysis of procollagen C-proteinase enhancer-1/glycosaminoglycan binding sites and of the potential role of calcium ions in the interaction. Int J Mol Sci, Special Issue: “Recent Developments on Protein–Ligand Interactions: From Structure, Function to Applications”. 2019, Vol. 20:5021.

Ilyechova E., Miliukhina I., Karpenko M., Orlov I., Puchkova L., Samsonov S.A. A case of Parkinson’s disease with early onset in a heterozygous carrier of mutation in Atp7b gene. J Pers Med. 2019, Vol. 9:41.

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.

Lubecka E.A., Karczynska A.S., Lipska A.G., Sieradzan A.K., Zieba K., Sikorska C., Uciechowska U.Samsonov S.A., Krupa P., Mozolewska M.A., Golon L., Gieldon A., Czaplewski C., Slusarz R., Slusarz M., Crivelli S.N., Liwo A. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. J Mol Graph Mod. 2019, Vol. 92:154–166.

Bojarski K.K., Becher J., Riemer T., Lemmnitzer K., Möller 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.

Samsonov S.A., Freza 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.

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.

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.

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.

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.

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.

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.

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, No. 32:7821–7827.

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.

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.

Zsila F., Samsonov S.A. Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis. Carb Res. 2018. 462:28–33.

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:e23103.

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. 1762:445–454.