{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T15:05:15Z","timestamp":1787238315466,"version":"build-2736575974"},"reference-count":95,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T00:00:00Z","timestamp":1680048000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"Narodowe Centrum Nauki","doi-asserted-by":"publisher","award":["UMO-2018\/30\/E\/ST4\/00037"],"award-info":[{"award-number":["UMO-2018\/30\/E\/ST4\/00037"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000921","name":"European Cooperation in Science and Technology","doi-asserted-by":"publisher","award":["CA 18103"],"award-info":[{"award-number":["CA 18103"]}],"id":[{"id":"10.13039\/501100000921","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP\u2019s molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.<\/jats:p>","DOI":"10.1021\/acs.jcim.2c01472","type":"journal-article","created":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T16:02:03Z","timestamp":1680105723000},"page":"2147-2157","source":"Crossref","is-referenced-by-count":25,"title":["Solvent Model Benchmark\nfor Molecular Dynamics of\nGlycosaminoglycans"],"prefix":"10.1021","volume":"63","author":[{"given":"Mateusz","family":"Marcisz","sequence":"first","affiliation":[{"name":"University of Gdan\u0301sk , , ul. Wita Stwosza 63 , ,","place":["Gdan\u0301sk, Poland, 80-308"]},{"name":"Intercollegiate Faculty of Biotechnology of UG and MUG , ul. Abrahama 58 , ,","place":["Gdan\u0301sk, Poland, 80-307"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5166-4849","authenticated-orcid":true,"given":"Sergey A.","family":"Samsonov","sequence":"additional","affiliation":[{"name":"University of Gdan\u0301sk , , ul. Wita Stwosza 63 , ,","place":["Gdan\u0301sk, Poland, 80-308"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2023,3,29]]},"reference":[{"key":"2026081804435821900_cit1","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2021.646808","article-title":"NMR Characterization of the Interactions Between Glycosaminoglycans\nand Proteins","volume":"8","author":"Bu","year":"2021","journal-title":"Front. Mol. 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Application to the Exploration of Glycosaminoglycan\nConformational Space","volume":"29","author":"Clerc","year":"2019","journal-title":"Glycobiology"},{"key":"2026081804435821900_cit5","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1369\/0022155420946403","article-title":"Glycosaminoglycan\u2013Protein\nInteractions: The First Draft of the Glycosaminoglycan Interactome","volume":"69","author":"Vallet","year":"2021","journal-title":"J. Histochem. Cytochem."},{"key":"2026081804435821900_cit6","doi-asserted-by":"publisher","first-page":"9152","DOI":"10.1021\/acs.chemrev.8b00354","article-title":"Proteoglycan\nChemical\nDiversity Drives Multifunctional Cell Regulation and Therapeutics","volume":"118","author":"Karamanos","year":"2018","journal-title":"Chem. 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Des."},{"key":"2026081804435821900_cit50","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1002\/prot.22076","article-title":"A Molecular\nDynamics Approach to\nStudy the Importance of Solvent in Protein Interactions","volume":"73","author":"Samsonov","year":"2008","journal-title":"Proteins: Struct., Funct., Genet."},{"key":"2026081804435821900_cit51","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1007\/978-1-4939-7756-7_22","article-title":"Computational\nAnalysis of Solvent Inclusion in Docking Studies of Protein\u2013Glycosaminoglycan\nSystems","volume-title":"Computational Drug Discovery and\nDesign","author":"Samsonov","year":"2018"},{"key":"2026081804435821900_cit52","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1093\/glycob\/7.5.597","article-title":"Molecular Dynamics Simulations of\nthe Two Disaccharides of Hyaluronan in Aqueous Solution","volume":"7","author":"Almond","year":"1997","journal-title":"Glycobiology"},{"key":"2026081804435821900_cit53","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1093\/glycob\/10.3.329","article-title":"Glycosaminoglycan\nConformation: Do Aqueous Molecular\nDynamics Simulations Agree with x-Ray Fiber Diffraction?","volume":"10","author":"Almond","year":"2000","journal-title":"Glycobiology"},{"key":"2026081804435821900_cit54","doi-asserted-by":"publisher","first-page":"4070","DOI":"10.1021\/acs.jctc.1c01172","article-title":"Generalized\nBorn Implicit Solvent Models Do Not Reproduce Secondary Structures\nof de Novo Designed Glu\/Lys Peptides","volume":"18","author":"Lang","year":"2022","journal-title":"J. Chem.\nTheory Comput."},{"key":"2026081804435821900_cit55","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.carres.2003.09.026","article-title":"Molecular\ndynamics simulation of a decasaccharide fragment\nof heparin in aqueous solution","volume":"339","author":"Verli","year":"2004","journal-title":"Carbohydr Res."},{"key":"2026081804435821900_cit56","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/jcc.20820","article-title":"GLYCAM06: A Generalizable\nBiomolecular Force Field. Carbohydrates","volume":"29","author":"Kirschner","year":"2008","journal-title":"J.\nComput. Chem."},{"key":"2026081804435821900_cit57","doi-asserted-by":"publisher","DOI":"10.1063\/1.4960175","article-title":"Accuracy Limit of\nRigid 3-Point Water Models","volume":"145","author":"Izadi","year":"2016","journal-title":"J. Chem. 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