{"id":"https://openalex.org/W4378783128","doi":"https://doi.org/10.1093/bioinformatics/btad350","title":"The ACPYPE web server for small-molecule MD topology generation","display_name":"The ACPYPE web server for small-molecule MD topology generation","publication_year":2023,"publication_date":"2023-05-30","ids":{"openalex":"https://openalex.org/W4378783128","doi":"https://doi.org/10.1093/bioinformatics/btad350","pmid":"https://pubmed.ncbi.nlm.nih.gov/37252824"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad350","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/6/btad350/50599896/btad350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/6/btad350/50599896/btad350.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062748725","display_name":"Luciano Porto Kagami","orcid":"https://orcid.org/0000-0002-4960-6500"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Luciano Kagami","raw_affiliation_strings":["Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB , Brussels 1050, Belgium"],"affiliations":[{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB , Brussels 1050, Belgium","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107938196","display_name":"Alan Wilter","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150574","display_name":"Moorfields Eye Hospital","ror":"https://ror.org/03tb37539","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I1325675289","https://openalex.org/I4210150574"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alan Wilter","raw_affiliation_strings":["Phenopolis Ltd & Moorfields Eye Hospital , London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Phenopolis Ltd & Moorfields Eye Hospital , London, United Kingdom","institution_ids":["https://openalex.org/I45129253","https://openalex.org/I4210150574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015435690","display_name":"Adri\u00e1n D\u00edaz","orcid":"https://orcid.org/0000-0003-0165-1318"},"institutions":[{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Adrian Diaz","raw_affiliation_strings":["Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB , Brussels 1050, Belgium","Structural biology Brussels, Vrije Universiteit Brussel , Brussels 1050, Belgium"],"affiliations":[{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB , Brussels 1050, Belgium","institution_ids":[]},{"raw_affiliation_string":"Structural biology Brussels, Vrije Universiteit Brussel , Brussels 1050, Belgium","institution_ids":["https://openalex.org/I13469542"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050454940","display_name":"Wim Vranken","orcid":"https://orcid.org/0000-0001-7470-4324"},"institutions":[{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Wim Vranken","raw_affiliation_strings":["Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB , Brussels 1050, Belgium","Structural biology Brussels, Vrije Universiteit Brussel , Brussels 1050, Belgium"],"affiliations":[{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB , Brussels 1050, Belgium","institution_ids":[]},{"raw_affiliation_string":"Structural biology Brussels, Vrije Universiteit Brussel , Brussels 1050, Belgium","institution_ids":["https://openalex.org/I13469542"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062748725"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":26.7456,"has_fulltext":true,"cited_by_count":177,"citation_normalized_percentile":{"value":0.99798008,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"39","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7779514789581299},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6611146330833435},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6611033082008362},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6324342489242554},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.6238348484039307},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6186589002609253},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5924393534660339},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5006582736968994},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.45518559217453003},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4507383108139038},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.4505957067012787},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.44528594613075256},{"id":"https://openalex.org/keywords/molecular-graphics","display_name":"Molecular graphics","score":0.44331467151641846},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.42323291301727295},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3277134895324707},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3173295855522156},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2602137327194214},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2524248957633972},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.25023746490478516},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.2433317005634308},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10624665021896362}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7779514789581299},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6611146330833435},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6611033082008362},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6324342489242554},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.6238348484039307},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6186589002609253},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5924393534660339},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5006582736968994},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.45518559217453003},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4507383108139038},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.4505957067012787},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.44528594613075256},{"id":"https://openalex.org/C126766683","wikidata":"https://www.wikidata.org/wiki/Q6896006","display_name":"Molecular graphics","level":3,"score":0.44331467151641846},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.42323291301727295},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3277134895324707},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3173295855522156},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2602137327194214},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2524248957633972},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25023746490478516},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.2433317005634308},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10624665021896362},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad350","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/6/btad350/50599896/btad350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37252824","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37252824","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10264366","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10264366","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10264366/pdf/btad350.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:vubissmart:VUBISSMART:2000:170193","is_oa":true,"landing_page_url":"https://biblio.vub.ac.be/vubir/the-acpype-web-server-for-smallmolecule-md-topology-generation(f9405468-81c8-44f4-9b1e-17beaaef9944).html","pdf_url":"https://biblio.vub.ac.be/vubirfiles/107079102/106606490.pdf","source":{"id":"https://openalex.org/S4306402573","display_name":"VUBIR (Vrije Universiteit Brussel)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I13469542","host_organization_name":"Vrije Universiteit Brussel","host_organization_lineage":["https://openalex.org/I13469542"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"publishedVersion"},{"id":"pmh:oai:vubissmart:VUBISSMART:2000:185266","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402573","display_name":"VUBIR (Vrije Universiteit Brussel)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I13469542","host_organization_name":"Vrije Universiteit Brussel","host_organization_lineage":["https://openalex.org/I13469542"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad350","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/6/btad350/50599896/btad350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6495604622","display_name":null,"funder_award_id":"I000323N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G6686177494","display_name":null,"funder_award_id":"G028821N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4378783128.pdf"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2054881399","https://openalex.org/W2070753604","https://openalex.org/W2147993766","https://openalex.org/W2150981663","https://openalex.org/W2170973067","https://openalex.org/W2171268876","https://openalex.org/W2763431406","https://openalex.org/W2949669744","https://openalex.org/W2995119220","https://openalex.org/W3095380161","https://openalex.org/W4205310241","https://openalex.org/W4206946001","https://openalex.org/W4310058955"],"related_works":["https://openalex.org/W4376877853","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W166480398","https://openalex.org/W1612808768","https://openalex.org/W167327709","https://openalex.org/W1977393088","https://openalex.org/W4387839566","https://openalex.org/W4210922265","https://openalex.org/W2288962794"],"abstract_inverted_index":{"The":[0],"web":[1],"application":[2],"is":[3],"freely":[4],"available":[5],"at":[6,15],"https://www.bio2byte.be/acpype/":[7],"and":[8],"the":[9],"open-source":[10],"code":[11],"can":[12],"be":[13],"found":[14],"https://github.com/alanwilter/acpype.":[16]},"counts_by_year":[{"year":2026,"cited_by_count":29},{"year":2025,"cited_by_count":95},{"year":2024,"cited_by_count":45},{"year":2023,"cited_by_count":8}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}
