Sergey Samsonov visited Unité en Sciences Biologiques et Biotechnologies (US2B) – UMR 6286 CNRS / University of Nantes and gave two talks.
US2B Website →Guilherme Justiniano Mizumoto, undergraduate student from the University of São Paulo joins us for two months. Welcome, Guilherme!
Sergey Samsonov (talk), Jacob Clark (talk) and Marta Pągielska (poster) participated in Tenth Polish-Korean Conference on "Protein Folding: Theoretical and Experimental Approaches". Gdańsk, Poland.
Event Website →Sergey Samsonov (dual talk with Prof. Zacharias from TUM), Jacob Clark (talk), Marta Pągielska (flash talk and poster) and Martina Kapica (poster) participated in The 22nd European Carbohydrate Symposium. Gdańsk, Poland.
Event Website →Sergey Samsonov (poster) participated in Beilstein Glycobioinformatics Symposium. Limburg, Germany.
Event Website →Nathalia Pavan, a Fahrenheit Scholarship Fellow, a PhD student from the University of São Paulo joins us for this year. Welcome, Nathalia!
Together with Dr. Wyrzykowski (University of Gdańsk) we obtained Fahrenheit Fellowship to host PhD student Nathalia Pavan from the group of prof. Valdecir Ximenes: https://unesp.br/portaldocentes/docentes/853, University of Sao Paulo (Brazil). The research project will be conducted in 2025.
Learn More →Sergey Samsonov (talk) and Marta Pągielska (poster) participated in the German Biophysical Society Meeting. Leipzig, Germany.
Event Website →Sergey Samsonov did his Visiting Researcher Fellowship (SMART LOIRE VALLEY PROGRAMME by Le Studium) https://www.lestudium-ias.com/fellows/sergey-samsonov at the laboratory of Prof. Fabien Lecaille https://www.univ-tours.fr/annuaire/m-fabien-lecaille at the University of Tours, France. During his visit he presented his work at the Center of Respiratory Pathologies Studies (University of Tours), at French Research Institute for Exploitation of the Sea in Nantes, participated in the Master’s Afternoon Talks at the Science Faculty at the University of Tours, Le Studium Thursday in Orleans https://www.lestudium-ias.com/events/glycosaminoglycans-cracking-new-biological-code-using-computers and together with prof. Czaplewski and Marta Pągielska organized and conducted the Workshop of Modeling at the Center of Respiratory Pathologies Studies.
Jacob Clark joined the group as a postdoc. Welcome!
Decrypting the "sulfation code" of glycosaminoglycans for understanding their function in the extracellular matrix. Funding Programme: OPUS from National Science Centre (Poland). Duration: 03.06.2024–02.06.2028. Budget: 2 128 604 PLN (494 000 EUR). Project Leader: Sergey Samsonov.
Project Page →Two National Science Centre projects Sonata Bis (Sonata Bis) and Beethoven (Beethoven) are over.
Marta Pągielska presented a poster at International Society of Quantum Biology and Pharmacology President Meeting 2024. Athens, Greece.
Event Website →“Exploring Protein/Glycosaminoglycan Interactions Through Experimental Data and Computational Models” at the Department of Theoretical Chemistry at the University of Gdańsk. Annemarie Danielsson.
“Modeling protein-glycosaminoglycan interactions in biologically relevant systems with the support of NMR approaches” at the seminar at Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw. Sergey Samsonov.
“Charged Connections: Quantum Parameterization of Calcium Cation - Heparin Interactions” at the Department of Theoretical Chemistry at the University of Gdańsk. Łukasz Golon.
Sergey Samsonov visited the group of prof. Ricard-Blum at the University of Lyon (France).
“Sulfation Code of Heparan Sulfate Proteoglycan Mimetics Modulating Cell Membrane Dynamics” at the Department of Theoretical Chemistry at the University of Gdańsk. Anila Sebastian.
Łukasz Golon, Annemarie Danielsson and Marta Pągielska participated in the conference “Frontiers of Coarse-Grained Models: From New Developments to Modeling Dynamics, Assemblies, and Macromolecular Machines” with posters (Łukasz Golon, Annemarie Danielsson ) and a talk (Marta Pągielska). Lyon, France.
Workshop Details →“Opracowanie i zastosowanie narzędzi do badań kompleksów glikozaminoglikany – biomolekuły” at the Faculty of Chemistry at the University of Gdańsk. Martyna Maszota-Zieleniak.
Anila Sebastian presented a talk at Joint Integrative Computational Biology workshop and CAPRI Meeting in Paris, France.
Sergey Samsonov gave invited talk “Computational approaches to understand protein-glycosaminoglycan recognition” at HS-Seq, Berlin Symposium. Berlin, Germany.
Anila Sebastian and Sergey Samsonov visited the group of prof. Daniel Huster at the University of Leipzig (Germany). Sergey Samsonov gave a talk “The dynamic dance: exploring protein-carbohydrate recognition with molecular dynamics” at the seminar at the Institute for Medical Physics and Biophysics.
Mateusz Marcisz defended his PhD Thesis “Development of the novel computational approaches for glycosaminoglycans” at the Faculty of Chemistry. Congratulations!
We hosted Prof. Serge Perez from University Grenoble Alpes, who presented at the Chemistry Faculty Seminar his talk “The algorithmic beauty of the starch granule” and discussed the ongoing projects with the group.
Annemarie Danielsson presented a poster at ELIXIR 3D BioInfo Community F2F/hybrid meeting in Prague, Czech Republic.
All our group participated in the 8th Polish-Korean Conference on Protein Folding. Jastrzębia Góra, Poland. Sergey Samsonov, Martyna Maszota-Zieleniak and Anila Sebastian gave talks, while Łukasz Golon, Mateusz Marcisz, Annemarie Danielsson and Marta Pągielska presented posters.
Marta Pągielska obtained her Bachelor’s Degree and will continue in the group as a Master student. Congratulations!
Małgorzata Kogut-Günthel defended her PhD Thesis “Computational Approaches to Characterise Biologically Active Systems Containing Proteins, Carbohydrates, and Ions” at the Faculty of Chemistry. Congratulations!
We hosted Prof. Satoru Tsushima from the University of Tokyo (Japan)/Helmholtz-Zentrum Dresden- Rossendorf (Germany). We discussed ongoing and future common projects.
Łukasz Golon joined the group as a postdoc. Welcome!
We hosted Prof. Daniel Huster and Dr. Anja Penk from the University of Leipzig (Germany). We discussed ongoing and future common projects.
Marta Pągielska visited the group of prof. Sylvie Ricard-Blum at the University of Lyon (France).
Mateusz Marcisz participated in the workshop (https://glycoalps.univ-grenoble-alpes.fr/glyco-club/glyco-club-s-activities/structural-glycoscience-summer-school-2023-886248.kjsp) l Structural GLycoscience Summer School 2023 in Grenoble (France) and visited the group of prof. Bertrand Huard at the University of Grenoble-Alpes (France).
Mateusz Marcisz the group of prof. Wonpil Im at the University of Lehigh (USA).
“Modeling glycosaminoglycan containing biologically relevant systems” at the Technical University of Munich (Germany). Sergey Samsonov.
Anila Sebastian joined the group as a postdoc. Welcome!
“One more little step towards understanding of glycosaminoglycan sulfation code” at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.
“SAXS data assisted modeling of the syndecan-2 and syndecan-4 proteoglycans - part II” at the Department of Theoretical Chemistry at the University of Gdańsk. Martyna Maszota-Zieleniak.
“Solvent models benchmark for molecular dynamics of glycosaminoglycans” at the Department of Theoretical Chemistry at the University of Gdańsk. Mateusz Marcisz.
“Simulation of Coarse-Grained Heparin in the SUGRES-1P force field - First Results” at the Department of Theoretical Chemistry at the University of Gdańsk. Annemarie Danielsson.
Sergey Samsonov visited the group of prof. Daniel Huster at the University of Leipzig (Germany).
We obtained a joint grant from a common program of NAWA (the Polish National Agency for Academic Exchange) and French Republic with the title “Characterization of protein-glycosaminoglycan interactions” together with the group of prof. Ricard-Blum at the University of Lyon (France).
We hosted Prof. Daniel Huster and Dr. Anja Penk from the University of Leipzig (Germany). We discussed ongoing and future common projects.
The 7th Polish-Korean Conference on Protein Folding. Seoul, South Korea. Poster presentation by Mateusz Marcicz. The poster presentation received an award as the best poster.
Chemistry Towards Biology (CTB10). Bratislava, Slovakia. Oral presentations “Computational and experimental analysis of the interactions between glycosaminoglycans and small molecules” by Martyna Maszota-Zieleniak and “Theoretical chemistry approaches to biologically relevant problems in the molecular systems containing glycosaminoglycans” by Sergey Samsonov.
Martyna Maszota-Zieleniak visited the group of prof. Ricard-Blum at the University of Lyon (France).
Margrethe Gaardløs visited the group of prof. Nikitovic at the University of Creete (Greece).
We hosted Dr. Georg Künze from the University of Leipzig (Germany). Within his visit, Dr. Künze gave a talk "Biomolecular Structure Determination by NMR Spectroscopy with Paramagnetic Metal Ions and Probes" at the Faculty of Chemistry. We also discussed ongoing and future common projects.
Sergey Samsonov visited the group of prof. Ricard-Blum at the University of Lyon (France).
European ROSETTACON on protein structure prediction and design. Warsaw, Poland. Oral presentations “Molecular Dynamics-based descriptors of 3-O-Sulfated Heparan Sulfate as Contributors of Protein Binding Specificity” by Annemarie Danielsson and “Cyclic peptide approach to model protein- glycosaminoglycan interactions” by Margrethe Gaardløs.
Innogly Annual Meeting 2022. Lugano, Switzerland. Invited talks “Repulsive Scaling Replica Exchange Molecular Dynamics in docking Glycosaminoglycans” by Mateusz Marcisz and “Modeling Biologically Relevant Interactions of Glycosaminoglycans” by Sergey Samsonov.
“Modeling protein-glycosaminoglycan interactions in biologically relevant systems” Intercollegiate Faculty of Biotechnology of University of Gdańsk/Medical University of Gdańsk. Sergey Samsonov.
“Molecular docking and simulations of GAG-protein interactions” at the Department of Theoretical Chemistry at the University of Gdańsk. Margrethe Gaardløs.
“Modeling molecular interactions of glycosaminoglycans” at the Lab of Theory of Biopolymers, University of Warsaw. Sergey Samsonov.
“Molecular Dynamics-based descriptors of Heparan Sulfate hexasaccharides” at the Department of Theoretical Chemistry at the University of Gdańsk. Annemarie Danielsson.
“Computational approaches to study glycosaminoglycan interactions” at the University of Leipzig (Germany). Sergey Samsonov.
Annemarie Danielsson, Margrethe Gaardløs and Sergey Samsonov visited the group of prof. Huster at the University of Leipzig (Germany).
“Computational analysis of ions interactions with proteins and glycosaminoglycas” at the Department of Theoretical Chemistry at the University of Gdańsk. Małgorzata Kogut.
We hosted Brianda Lopez Santini from the group of prof. Zacharias at the Technical University of Munich within the DAAD/NAWA German-Polish Exchange Programme.
Online Workshop: “Computational Modeling in Chemistry, Biology and Materials - Making it Mainstream” (https://sites.google.com/cusat.ac.in/workshop/home). Talk "Modeling glycosaminoglycans: advances and challenges" by Sergey Samsonov.
Krzysztof Bojarski defended his PhD Thesis “Computational approaches to study protein- glycosaminoglycan systems” at the Faculty of Chemistry. Congratulations!
The 6th Polish-Korean Conference on Protein Folding. Jastrzębia Góra, Poland. Invited talk by Sergey Samsonov, short lectures by Martyna Maszota-Zieleniak, Mateusz Marcisz, Margrethe Gaardløs and Krzysztof Bojarski, posters by Małgorzata Kogut and Annemarie Danielsson.
Hybrid Symposium “GlycosAminoGlycans: What remains to be solved?”, Heraklion, Greece. Talk: “Challenges and advances in molecular docking of glycosaminoglycans” by Sergey Samsonov.
Online seminar at VCU Medical Chemistry Department, Virginia Commonwealth University, USA. Talk “Challenges and advances in molecular docking of glycosaminoglycans” by Sergey Samsonov.
Margrethe Gaardløs joined the group as a postdoc.
We participated in the online workshop on Computational Analysis Tools (CAT) provided by Dr. Martin Frank (glycosciences.deö Biognow AB Göteborg, Sweden)
“Modeling molecular interactions of glycosaminoglycans” at the Technical University of Munich (Germany). Sergey Samsonov and Krzysztof Bojarski
Krzysztof Bojarski and Sergey Samsonov visited the group of prof. Zacharias at the Technical University of Munich (Germany) on 12-15.07.2021 and 16.06-15.07.2021, respectively.
Online Joint Warren and Beilstein Symposium on Glycosciences. Talk "Computational insights into modeling protein-glycosaminoglycan interactions" by Sergey Samsonov.
“Even more glycosaminoglycans: ongoing projects” at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.
“The Specificity of Interaction of Interleukin-8 with Glycosaminoglycans: Comparison with Acidic Peptides” at the Department of Theoretical Chemistry at the University of Gdańsk. Annemarie Danielsson.
“Glycosaminoglycans in modeling: does the size matter?” at the Department of Theoretical Chemistry at the University of Gdańsk. Mateusz Marcisz. “Computational approaches to study protein-glycosaminoglycan systems” at the Department of Theoretical Chemistry at the University of Gdańsk. Krzysztof Bojarski.
“Glycosaminoglycans in modeling: does the size matter?” at the Department of Theoretical Chemistry at the University of Gdańsk. Mateusz Marcisz.
"Modeling biologically relevant interactions with glycosaminoglycans” at the Faculty of Chemistry at the University of Gdańsk. Sergey Samsonov.
“Evaluation of Replica Exchange with Repulsive Scaling Approach for Docking Glycosaminoglycans” at the Department of Theoretical Chemistry at the University of Gdańsk. Martyna Maszota-Zieleniak.
“Computational approaches to study protein-glycosaminoglycan systems” at the Department of Theoretical Chemistry at the University of Gdańsk. Krzysztof Bojarski.
We obtained a joint grant from a common program of DAAD (The German Academic Exchange Service) and NAWA (the Polish National Agency for Academic Exchange) with the title “Advanced and innovative computational approaches to study protein-glycosaminoglycan systems” together with the group of prof. Zacharias at the Technical University of Munich.
“Computational insights into the role of ions in protein-glycosaminoglycan systems” at the Department of Theoretical Chemistry at the University of Gdańsk. Małgorzata Kogut.
The first Pomeranian Student Chemial Symposium 2020. Poster presentation “The effect of GAG chain polarity on its interactions with proteins” (in Polish) by Krzysztof Bojarski.
Annemarie Danielsson joined the group as a PhD student. Welcome!
“Modeling AlgE4 and alginate interactions” at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.
“April protein and GAGs” at the Department of Theoretical Chemistry at the University of Gdańsk. Mateusz Marcisz.
Małgorzata Kogut joined the group as a PhD student. Welcome!
34th Molecular Modelling Workshop 2020 (Erlangen, Germany). Talk “Challenges in modeling protein-glycosaminoglycan systems” by Krzysztof Bojarski.
We hosted dr. Aleksei Sysa from International Sakharov Environmental Institute (Minsk, Belarus). We also discussed ongoing and future common projects.
We hosted Prof. Sylvie Ricard-Blum from the University of Lyon (France). Within her visit, Prof. Ricard-Blum gave a talk "Extracellular glycosaminoglycan-binding proteins: from structure to interactions" at the Faculty of Chemistry. We also discussed ongoing and future common projects.
“The progress in Sonata Bis project." at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.
“Glycosaminoglycan binding: specific or not?” at the Technical University of Munich (Germany). Sergey Samsonov.
Martyna Maszota-Zieleniak joined the group as a Postdoctoral Researcher. Welcome!
Mateusz Marcisz joined the group as a PhD student. Welcome!
5-th Polish - Korean Conference on Protein Folding (Seoul, Korea). Talk “Modeling insights into glycosaminoglycan biologically relevant functions” by Sergey Samsonov. Talk “(Pro)cathepsins and glycosaminoglycans – the significance of their complexes in biological systems” by Krzysztof Bojarski.
XXth European Carbohydrate Symposium (Leiden, the Netherlands). Talk “Modeling insights into molecular mechanisms underlying the role of glycosaminoglycans in cell signaling processes” by Sergey Samsonov. Poster presentation “Does a microsecond timescale molecular dynamics simulation provide a deeper view on protein-glycosaminoglycan system?” by Krzysztof Bojarski.
Workshop Multiscale Modeling, Lorentz Symposium (Leiden, the Netherlands). Poster presentation “Glycosaminoglycan Coarse-Grained Models” by Sergey Samsonov.
Sakharov Reading 2019: Environmental Problems of XXI century (Minsk, Belarus). Talk “Cathepsins, glycosaminoglycans and biological role of their interactions” by Krzysztof Bojarski; talk “Modeling glycosaminoglycans – key molecules for tissue regeneration” by Sergey Samsonov. Co-organization of the event by Sergey Samsonov.
“Polonez project. Summary" at the Department of Theoretical Chemistry at the University of Gdańsk. Sergey Samsonov.
Modeling protein-glycosaminoglycan interactions" at International Sakharov Environmental Institute (Minsk, Belarus). Sergey Samsonov.
Jan Potthoff from the Free University of Berlin joined our group within the Erasmus Programme.