SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. - Joan Teyra; Sergey A. Samsonov; Sven Schreiber; M. Teresa Pisabarro (BMC Bioinform., 2011)

Docking glycosaminoglycans to proteins: analysis of solvent inclusion. - Sergey A. Samsonov; Joan Teyra; M. Teresa Pisabarro (J. Comput. Aided Mol. Des., 2011)

Flexibility and Explicit Solvent in Molecular-Dynamics-Based Docking of Protein-Glycosaminoglycan Systems. - Sergey A. Samsonov; Jan-Philip Gehrcke; M. Teresa Pisabarro (J. Chem. Inf. Model., 2014)

Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility. - Joséphine Abi-Ghanem; Sergey A. Samsonov; M. Teresa Pisabarro (J. Comput. Aided Mol. Des., 2015)

Coarse-Grained Model of Glycosaminoglycans. - Sergey A. Samsonov; Leon Bichmann; M. Teresa Pisabarro (J. Chem. Inf. Model., 2015)

The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from a Combined Bioinformatical and Experimental Approach. - Gerd Anders; Ulrich Hassiepen; Stephan Theisgen; Stephan Heymann; Lionel Muller; Tania Panigada; Daniel Huster; Sergey A. Samsonov (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Modeling large protein-glycosaminoglycan complexes using a fragment-based approach. - Sergey A. Samsonov; Martin Zacharias; Isaure Chauvot de Beauchêne (J. Comput. Chem., 2019)

Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study. - Krzysztof K. Bojarski; Agnieszka S. Karczynska; Sergey A. Samsonov (J. Chem. Inf. Model., 2020)

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. - Agnieszka S. Karczynska; Karolina Zieba; Urszula Uciechowska; Magdalena A. Mozolewska; Pawel Krupa; Emilia A. Lubecka; Agnieszka G. Lipska; Celina Sikorska; Sergey A. Samsonov; Adam K. Sieradzan; Artur Gieldon; Adam Liwo; et al. (J. Chem. Inf. Model., 2020)

Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans. - Martyna Maszota-Zieleniak; Mateusz Marcisz; Malgorzata M. Kogut; Till Siebenmorgen; Martin Zacharias; Sergey A. Samsonov (J. Comput. Chem., 2021)

Role of Oligosaccharide Chain Polarity in Protein-Glycosaminoglycan Interactions. - Krzysztof K. Bojarski; Sergey A. Samsonov (J. Chem. Inf. Model., 2021)

Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter? - Mateusz Marcisz; Martin Zacharias; Sergey A. Samsonov (J. Chem. Inf. Model., 2021)

Molecular dynamics-based descriptors of 3-O-Sulfated Heparan sulfate as contributors of protein binding specificity. - Annemarie Danielsson; Malgorzata M. Kogut; Martyna Maszota-Zieleniak; Pradeep Chopra; Geert-Jan Boons; Sergey A. Samsonov (Comput. Biol. Chem., 2022)

Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis. - Malgorzata M. Kogut; Annemarie Danielsson; Sylvie Ricard-Blum; Sergey A. Samsonov (Comput. Biol. Chem., 2022)

Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. - Mateusz Marcisz; Margrethe Gaardløs; Krzysztof K. Bojarski; Till Siebenmorgen; Martin Zacharias; Sergey A. Samsonov (J. Comput. Chem., 2022)

Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. - Mateusz Marcisz; Sergey A. Samsonov (J. Chem. Inf. Model., 2023)

Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes. - Sebastian Anila; Sergey A. Samsonov (J. Chem. Inf. Model., 2024)