{"id":"https://openalex.org/W4392193585","doi":"https://doi.org/10.1021/acs.jcim.4c00030","title":"Benchmarking Water Models in Molecular Dynamics of Protein\u2013Glycosaminoglycan Complexes","display_name":"Benchmarking Water Models in Molecular Dynamics of Protein\u2013Glycosaminoglycan Complexes","publication_year":2024,"publication_date":"2024-02-27","ids":{"openalex":"https://openalex.org/W4392193585","doi":"https://doi.org/10.1021/acs.jcim.4c00030","pmid":"https://pubmed.ncbi.nlm.nih.gov/38410841"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00030","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00030","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c00030","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c00030","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018904186","display_name":"Sebastian Anila","orcid":"https://orcid.org/0000-0002-8444-1326"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Sebastian Anila","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086671958","display_name":"Sergey A. Samsonov","orcid":"https://orcid.org/0000-0002-5166-4849"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Sergey A. Samsonov","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland"],"raw_orcid":"https://orcid.org/0000-0002-5166-4849","affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, ul. Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086671958"],"corresponding_institution_ids":["https://openalex.org/I40413290"],"apc_list":null,"apc_paid":null,"fwci":4.8707,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.96143646,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"64","issue":"5","first_page":"1691","last_page":"1703"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11131","display_name":"Proteoglycans and glycosaminoglycans research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11131","display_name":"Proteoglycans and glycosaminoglycans research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10831","display_name":"Cell Adhesion Molecules Research","score":0.9850999712944031,"subfield":{"id":"https://openalex.org/subfields/2723","display_name":"Immunology and Allergy"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9778000116348267,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6510347127914429},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6270352602005005},{"id":"https://openalex.org/keywords/glycosaminoglycan","display_name":"Glycosaminoglycan","score":0.5595932602882385},{"id":"https://openalex.org/keywords/glycan","display_name":"Glycan","score":0.4701766073703766},{"id":"https://openalex.org/keywords/galectin","display_name":"Galectin","score":0.4591369926929474},{"id":"https://openalex.org/keywords/heparan-sulfate","display_name":"Heparan sulfate","score":0.4564599394798279},{"id":"https://openalex.org/keywords/self-healing-hydrogels","display_name":"Self-healing hydrogels","score":0.4163368046283722},{"id":"https://openalex.org/keywords/chondroitin","display_name":"Chondroitin","score":0.4150247871875763},{"id":"https://openalex.org/keywords/hyaluronic-acid","display_name":"Hyaluronic acid","score":0.4119843542575836},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3914811611175537},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.34236323833465576},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.20465779304504395},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14850148558616638},{"id":"https://openalex.org/keywords/glycoprotein","display_name":"Glycoprotein","score":0.12661239504814148}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6510347127914429},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6270352602005005},{"id":"https://openalex.org/C153074725","wikidata":"https://www.wikidata.org/wiki/Q407553","display_name":"Glycosaminoglycan","level":2,"score":0.5595932602882385},{"id":"https://openalex.org/C206212055","wikidata":"https://www.wikidata.org/wiki/Q2553138","display_name":"Glycan","level":3,"score":0.4701766073703766},{"id":"https://openalex.org/C156293190","wikidata":"https://www.wikidata.org/wiki/Q83138026","display_name":"Galectin","level":2,"score":0.4591369926929474},{"id":"https://openalex.org/C2778041096","wikidata":"https://www.wikidata.org/wiki/Q424668","display_name":"Heparan sulfate","level":3,"score":0.4564599394798279},{"id":"https://openalex.org/C108586683","wikidata":"https://www.wikidata.org/wiki/Q17164826","display_name":"Self-healing hydrogels","level":2,"score":0.4163368046283722},{"id":"https://openalex.org/C2776735749","wikidata":"https://www.wikidata.org/wiki/Q4862650","display_name":"Chondroitin","level":3,"score":0.4150247871875763},{"id":"https://openalex.org/C2777529286","wikidata":"https://www.wikidata.org/wiki/Q337231","display_name":"Hyaluronic acid","level":2,"score":0.4119843542575836},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3914811611175537},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.34236323833465576},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.20465779304504395},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14850148558616638},{"id":"https://openalex.org/C108625454","wikidata":"https://www.wikidata.org/wiki/Q187126","display_name":"Glycoprotein","level":2,"score":0.12661239504814148},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006493","descriptor_name":"Heparin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c00030","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00030","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c00030","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38410841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38410841","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10934818","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10934818","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10934818/pdf/ci4c00030.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c00030","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00030","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c00030","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8600000143051147,"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6"}],"awards":[{"id":"https://openalex.org/G3234076458","display_name":null,"funder_award_id":"UMO-2018/31/G/ST4/00246","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392193585.pdf"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W777706533","https://openalex.org/W1539262497","https://openalex.org/W1840163537","https://openalex.org/W1976499671","https://openalex.org/W1983659112","https://openalex.org/W1986012385","https://openalex.org/W1994974479","https://openalex.org/W2004596698","https://openalex.org/W2019574809","https://openalex.org/W2024726841","https://openalex.org/W2025556412","https://openalex.org/W2025880126","https://openalex.org/W2028702957","https://openalex.org/W2029667189","https://openalex.org/W2032853185","https://openalex.org/W2032917778","https://openalex.org/W2049475242","https://openalex.org/W2052299578","https://openalex.org/W2054732153","https://openalex.org/W2055881436","https://openalex.org/W2058052041","https://openalex.org/W2066690664","https://openalex.org/W2067174909","https://openalex.org/W2081850717","https://openalex.org/W2087596773","https://openalex.org/W2092749292","https://openalex.org/W2106140689","https://openalex.org/W2121076289","https://openalex.org/W2130673759","https://openalex.org/W2145631950","https://openalex.org/W2153703984","https://openalex.org/W2156297944","https://openalex.org/W2164270482","https://openalex.org/W2166211977","https://openalex.org/W2211272170","https://openalex.org/W2329540625","https://openalex.org/W2332712348","https://openalex.org/W2392674489","https://openalex.org/W2462618639","https://openalex.org/W2510867035","https://openalex.org/W2526990955","https://openalex.org/W2582743722","https://openalex.org/W2586101801","https://openalex.org/W2735619894","https://openalex.org/W2773728373","https://openalex.org/W2890624098","https://openalex.org/W2894134508","https://openalex.org/W2922133186","https://openalex.org/W2954153470","https://openalex.org/W2960448439","https://openalex.org/W2964365474","https://openalex.org/W3040006904","https://openalex.org/W3105643282","https://openalex.org/W3211314960","https://openalex.org/W3215372575","https://openalex.org/W4211225699","https://openalex.org/W4221029688","https://openalex.org/W4281675815","https://openalex.org/W4284666358","https://openalex.org/W4322764495","https://openalex.org/W4361296857"],"related_works":["https://openalex.org/W2067074405","https://openalex.org/W1995003331","https://openalex.org/W2010483968","https://openalex.org/W2025713273","https://openalex.org/W2129382287","https://openalex.org/W2469499048","https://openalex.org/W2083556833","https://openalex.org/W1972092441","https://openalex.org/W2316236125","https://openalex.org/W2913256058"],"abstract_inverted_index":{"Glycosaminoglycans":[0],"(GAGs)":[1],"made":[2],"of":[3,19,27,36,55,63,73,94,107,119,138,171,180,199,241,244,251],"repeating":[4],"disaccharide":[5],"units":[6],"intricately":[7],"engage":[8],"with":[9,211],"proteins,":[10],"playing":[11],"a":[12,34,116],"crucial":[13],"role":[14],"in":[15,30,68,102,123,142,227,235],"the":[16,20,25,49,61,64,69,74,82,92,99,136,139,178,192,233,239,242,248],"spatial":[17],"organization":[18],"extracellular":[21],"matrix":[22],"(ECM)":[23],"and":[24,52,60,86,153,155,163,185,194,208,218],"transduction":[26],"biological":[28],"signals":[29],"cells":[31],"to":[32,114,134,167,176,231],"modulate":[33],"number":[35],"biochemical":[37],"processes.":[38],"Exploring":[39],"protein-GAG":[40,70,77,108,140,181],"interactions":[41,78,198],"reveals":[42],"several":[43,200],"challenges":[44],"for":[45,126,191,247],"their":[46,57],"analysis,":[47],"namely,":[48],"highly":[50],"charged":[51],"periodic":[53],"nature":[54],"GAGs,":[56,195],"multipose":[58],"binding,":[59],"abundance":[62],"interfacial":[65],"water":[66,84,96,121,165,245],"molecules":[67],"complexes.":[71,109,182,253],"Most":[72],"studies":[75],"on":[76,91,98],"are":[79,88,173,222],"conducted":[80],"using":[81,145],"TIP3P":[83],"model,":[85],"there":[87],"no":[89],"data":[90],"effect":[93],"various":[95],"models":[97,122,166,246],"results":[100],"obtained":[101],"molecular":[103],"dynamics":[104,179],"(MD)":[105],"simulations":[106,125,144],"Hence,":[110],"it":[111],"is":[112],"essential":[113],"perform":[115],"systematic":[117],"analysis":[118],"different":[120,146,228],"MD":[124,143,249],"these":[127,236,252],"systems.":[128],"In":[129],"this":[130],"work,":[131],"we":[132],"aim":[133],"evaluate":[135],"properties":[137],"complexes":[141,237],"explicit:":[147],"TIP3P,":[148],"SPC/E,":[149],"TIP4P,":[150],"TIP4PEw,":[151],"OPC,":[152],"TIP5P":[154],"implicit:":[156],"IGB":[157],"=":[158],"1,":[159],"2,":[160],"5,":[161],"7,":[162],"8":[164],"find":[168],"out":[169],"which":[170],"them":[172],"best":[174],"suited":[175],"study":[177,232],"The":[183,197,224],"FF14SB":[184],"GLYCAM06":[186],"force":[187],"fields":[188],"were":[189],"used":[190,230],"proteins":[193],"respectively.":[196],"GAG":[201],"types,":[202],"such":[203],"as":[204],"heparin,":[205],"chondroitin":[206],"sulfate,":[207],"hyaluronic":[209],"acid":[210],"basic":[212],"fibroblast":[213],"growth":[214],"factor,":[215],"cathepsin":[216],"K,":[217],"CD44":[219],"receptor,":[220],"respectively,":[221],"investigated.":[223],"observed":[225],"variations":[226],"descriptors":[229],"binding":[234],"emphasize":[238],"relevance":[240],"choice":[243],"simulation":[250]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":5}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}