{"id":"https://openalex.org/W4409566737","doi":"https://doi.org/10.1021/acs.jcim.5c00165","title":"Structural Systems Biology Toolkit (SSBtoolkit): From Molecular Structure to Subcellular Signaling Pathways","display_name":"Structural Systems Biology Toolkit (SSBtoolkit): From Molecular Structure to Subcellular Signaling Pathways","publication_year":2025,"publication_date":"2025-04-18","ids":{"openalex":"https://openalex.org/W4409566737","doi":"https://doi.org/10.1021/acs.jcim.5c00165","pmid":"https://pubmed.ncbi.nlm.nih.gov/40248991"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00165","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00165","pdf_url":null,"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":null,"license_id":null,"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","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://juser.fz-juelich.de/record/1059616","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031575323","display_name":"Rui Pedro Ribeiro","orcid":"https://orcid.org/0000-0001-9939-2013"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rui Pedro Ribeiro","raw_affiliation_strings":["Department of Biotechnology","University of Verona"],"raw_orcid":"https://orcid.org/0000-0001-9939-2013","affiliations":[{"raw_affiliation_string":"Department of Biotechnology","institution_ids":[]},{"raw_affiliation_string":"University of Verona","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041456754","display_name":"Jonas Go\u00dfen","orcid":"https://orcid.org/0000-0002-0730-6796"},"institutions":[{"id":"https://openalex.org/I143379178","display_name":"FZI Research Center for Information Technology","ror":"https://ror.org/04kdh6x72","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I143379178"]},{"id":"https://openalex.org/I4210093057","display_name":"Faculty (United Kingdom)","ror":"https://ror.org/00qpxe165","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210093057"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"Jonas Go\u00dfen","raw_affiliation_strings":["Computer Science and Natural Sciences RWTH Aachen University","Faculty of Mathematics","Forschungszentrum","IAS-5/INM-9"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Natural Sciences RWTH Aachen University","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Faculty of Mathematics","institution_ids":["https://openalex.org/I4210093057"]},{"raw_affiliation_string":"Forschungszentrum","institution_ids":["https://openalex.org/I143379178"]},{"raw_affiliation_string":"IAS-5/INM-9","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026564872","display_name":"Giulia Rossetti","orcid":"https://orcid.org/0000-0002-2032-4630"},"institutions":[{"id":"https://openalex.org/I143379178","display_name":"FZI Research Center for Information Technology","ror":"https://ror.org/04kdh6x72","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I143379178"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Giulia Rossetti","raw_affiliation_strings":["Department of Neurology","Forschungszentrum","IAS-5/INM-9","J\u00fclich Supercomputing Center, Forschungszentrum","University Hospital RWTH Aachen"],"raw_orcid":"https://orcid.org/0000-0002-2032-4630","affiliations":[{"raw_affiliation_string":"Department of Neurology","institution_ids":[]},{"raw_affiliation_string":"Forschungszentrum","institution_ids":["https://openalex.org/I143379178"]},{"raw_affiliation_string":"IAS-5/INM-9","institution_ids":[]},{"raw_affiliation_string":"J\u00fclich Supercomputing Center, Forschungszentrum","institution_ids":[]},{"raw_affiliation_string":"University Hospital RWTH Aachen","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101510898","display_name":"Alejandro Giorgetti","orcid":"https://orcid.org/0000-0001-8738-6150"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I143379178","display_name":"FZI Research Center for Information Technology","ror":"https://ror.org/04kdh6x72","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I143379178"]}],"countries":["DE","IT"],"is_corresponding":true,"raw_author_name":"Alejandro Giorgetti","raw_affiliation_strings":["Department of Biotechnology","Forschungszentrum","IAS-5/INM-9","University of Verona"],"raw_orcid":"https://orcid.org/0000-0001-8738-6150","affiliations":[{"raw_affiliation_string":"Department of Biotechnology","institution_ids":[]},{"raw_affiliation_string":"Forschungszentrum","institution_ids":["https://openalex.org/I143379178"]},{"raw_affiliation_string":"IAS-5/INM-9","institution_ids":[]},{"raw_affiliation_string":"University of Verona","institution_ids":["https://openalex.org/I119439378"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101510898"],"corresponding_institution_ids":["https://openalex.org/I119439378","https://openalex.org/I143379178"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07722178,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"9","first_page":"4257","last_page":"4262"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9958000183105469,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9952999949455261,"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/systems-biology","display_name":"Systems biology","score":0.6026319265365601},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.570000410079956},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.5072307586669922},{"id":"https://openalex.org/keywords/structural-biology","display_name":"Structural biology","score":0.46303921937942505},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3898756504058838},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.389814168214798},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3476528227329254}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6026319265365601},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.570000410079956},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.5072307586669922},{"id":"https://openalex.org/C191120209","wikidata":"https://www.wikidata.org/wiki/Q908902","display_name":"Structural biology","level":2,"score":0.46303921937942505},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3898756504058838},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.389814168214798},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3476528227329254}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042541","descriptor_name":"Intracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D042541","descriptor_name":"Intracellular Space","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.5c00165","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00165","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40248991","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40248991","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:juser.fz-juelich.de:1059616","is_oa":true,"landing_page_url":"https://juser.fz-juelich.de/record/1059616","pdf_url":null,"source":{"id":"https://openalex.org/S4306401090","display_name":"JuSER (Forschungszentrum J\u00fclich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I171892758","host_organization_name":"Forschungszentrum J\u00fclich","host_organization_lineage":["https://openalex.org/I171892758"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling 65(9), 4257 - 4262 (2025). doi:10.1021/acs.jcim.5c00165","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:publications.rwth-aachen.de:1031533","is_oa":false,"landing_page_url":"https://publications.rwth-aachen.de/record/1031533","pdf_url":null,"source":{"id":"https://openalex.org/S4306401362","display_name":"RWTH Publications (RWTH Aachen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887968799","host_organization_name":"RWTH Aachen University","host_organization_lineage":["https://openalex.org/I887968799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of chemical information and modeling 65(9), 4257-4262 (2025). doi:10.1021/acs.jcim.5c00165","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.34734/fzj-2026-03479","is_oa":true,"landing_page_url":"https://doi.org/10.34734/fzj-2026-03479","pdf_url":null,"source":{"id":"https://openalex.org/S7407051455","display_name":"JuSER Publikationsportal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:juser.fz-juelich.de:1059616","is_oa":true,"landing_page_url":"https://juser.fz-juelich.de/record/1059616","pdf_url":null,"source":{"id":"https://openalex.org/S4306401090","display_name":"JuSER (Forschungszentrum J\u00fclich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I171892758","host_organization_name":"Forschungszentrum J\u00fclich","host_organization_lineage":["https://openalex.org/I171892758"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling 65(9), 4257 - 4262 (2025). doi:10.1021/acs.jcim.5c00165","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3936970252","display_name":null,"funder_award_id":"#945539","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G455327546","display_name":null,"funder_award_id":"PE0000006","funder_id":"https://openalex.org/F7311471023","funder_display_name":"NextGenerationEU"}],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F7311471023","display_name":"NextGenerationEU","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1509385305","https://openalex.org/W2024725429","https://openalex.org/W2041265238","https://openalex.org/W2049445311","https://openalex.org/W2056799530","https://openalex.org/W2080486913","https://openalex.org/W2084527991","https://openalex.org/W2097240335","https://openalex.org/W2102653059","https://openalex.org/W2104136496","https://openalex.org/W2129507956","https://openalex.org/W2134967712","https://openalex.org/W2137312021","https://openalex.org/W2566980643","https://openalex.org/W2607348308","https://openalex.org/W2736977076","https://openalex.org/W2784213390","https://openalex.org/W2804603144","https://openalex.org/W2964492976","https://openalex.org/W2985085174","https://openalex.org/W2985350006","https://openalex.org/W2988361147","https://openalex.org/W2991436132","https://openalex.org/W3008279928","https://openalex.org/W3043528025","https://openalex.org/W3097145107","https://openalex.org/W4205963581","https://openalex.org/W4211246989","https://openalex.org/W4312094047","https://openalex.org/W4385198189"],"related_works":["https://openalex.org/W2057769265","https://openalex.org/W2802815821","https://openalex.org/W2077919099","https://openalex.org/W631732704","https://openalex.org/W2155261113","https://openalex.org/W5284979","https://openalex.org/W2081231176","https://openalex.org/W4245853730","https://openalex.org/W2508318930","https://openalex.org/W1981076832"],"abstract_inverted_index":{"Here,":[0],"we":[1],"introduce":[2],"the":[3,36,44,47,54,57,64,68,90,95,106,116,123,127],"Structural":[4],"Systems":[5],"Biology":[6],"(SSB)":[7],"toolkit,":[8],"a":[9],"Python":[10],"library":[11],"that":[12],"integrates":[13],"structural":[14],"macromolecular":[15],"data":[16],"with":[17,63],"systems":[18],"biology":[19],"simulations":[20],"to":[21,88],"model":[22],"signal-transduction":[23,48],"pathways":[24],"of":[25,35,39,46,56,70,92,98,108,115],"G-protein-coupled":[26],"receptors":[27],"(GPCRs).":[28],"Our":[29],"framework":[30],"streamlines":[31],"simulation":[32],"and":[33,126,130],"analysis":[34],"mathematical":[37],"models":[38],"GPCRs":[40],"cellular":[41,129],"pathways,":[42],"facilitating":[43],"exploration":[45],"kinetics":[49],"induced":[50],"by":[51],"ligand-GPCR":[52],"interactions:":[53],"dose\u2013response":[55],"ligand":[58,99],"can":[59],"be":[60],"modeled,":[61],"along":[62],"corresponding":[65],"change":[66],"in":[67,105],"concentration":[69],"other":[71],"signaling":[72],"molecular":[73,124],"species":[74],"over":[75],"time,":[76],"like":[77],"for":[78],"instance":[79],"[Ca":[80],"2+":[81],"]":[82],"or":[83],"[cAMP].":[84],"SSB":[85],"toolkit":[86],"brings":[87],"light":[89],"possibility":[91],"easily":[93],"investigating":[94],"subcellular":[96],"effects":[97],"binding":[100],"on":[101],"receptor":[102],"activation,":[103],"even":[104],"presence":[107],"genetic":[109],"mutations,":[110],"thereby":[111],"enhancing":[112],"our":[113],"understanding":[114],"intricate":[117],"relationship":[118],"between":[119],"ligand\u2013target":[120],"interactions":[121],"at":[122],"level":[125],"higher-level":[128],"(patho)physiological":[131],"response":[132],"mechanisms.":[133]},"counts_by_year":[],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}