{"id":"https://openalex.org/W4413847180","doi":"https://doi.org/10.1371/journal.pcbi.1013422","title":"SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides","display_name":"SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides","publication_year":2025,"publication_date":"2025-08-29","ids":{"openalex":"https://openalex.org/W4413847180","doi":"https://doi.org/10.1371/journal.pcbi.1013422","pmid":"https://pubmed.ncbi.nlm.nih.gov/40880496"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013422","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013422","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013422&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013422&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119484526","display_name":"Maryam Ghobakhloo","orcid":null},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Maryam Ghobakhloo","raw_affiliation_strings":["Department of Cell and Developmental Biology, School of Biological Sciences, College of Science, University of Tehran, Tehran, Iran"],"raw_orcid":"https://orcid.org/0009-0002-0040-7153","affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, School of Biological Sciences, College of Science, University of Tehran, Tehran, Iran","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012715487","display_name":"Zahra Ghorbanali","orcid":"https://orcid.org/0000-0003-4809-1311"},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Zahra Ghorbanali","raw_affiliation_strings":["Computational Biology Research Center (CBRC), Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran"],"raw_orcid":"https://orcid.org/0000-0003-4809-1311","affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067478126","display_name":"Fatemeh Zare\u2010Mirakabad","orcid":"https://orcid.org/0000-0003-2849-3778"},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Fatemeh Zare-Mirakabad","raw_affiliation_strings":["Computational Biology Research Center (CBRC), Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran"],"raw_orcid":"https://orcid.org/0000-0003-2849-3778","affiliations":[{"raw_affiliation_string":"Computational Biology Research Center (CBRC), Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005130899","display_name":"Roya Abbaszadeh","orcid":null},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Roya Abbaszadeh","raw_affiliation_strings":["Department of Biology, Philipps-University Marburg, Marburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Philipps-University Marburg, Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119484527","display_name":"Mohammad Taheri-Ledari","orcid":null},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Mohammad Taheri-Ledari","raw_affiliation_strings":["Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran"],"raw_orcid":"https://orcid.org/0009-0007-9132-077X","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5119484528","display_name":"Bahman Zeynali","orcid":null},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Bahman Zeynali","raw_affiliation_strings":["Department of Cell and Developmental Biology, School of Biological Sciences, College of Science, University of Tehran, Tehran, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, School of Biological Sciences, College of Science, University of Tehran, Tehran, Iran","institution_ids":["https://openalex.org/I23946033"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005130899","https://openalex.org/A5012715487","https://openalex.org/A5067478126","https://openalex.org/A5119484526","https://openalex.org/A5119484527","https://openalex.org/A5119484528"],"corresponding_institution_ids":["https://openalex.org/I158248296","https://openalex.org/I161103922","https://openalex.org/I23946033"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1441,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.77888027,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"21","issue":"8","first_page":"e1013422","last_page":"e1013422"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9958999752998352,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9958999752998352,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9797999858856201,"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/T11561","display_name":"Protein Hydrolysis and Bioactive Peptides","score":0.9739000201225281,"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":0.5280333757400513},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4367489516735077},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3729134798049927},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25900956988334656}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5280333757400513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4367489516735077},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3729134798049927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25900956988334656}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002364","descriptor_name":"Caseins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002364","descriptor_name":"Caseins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002364","descriptor_name":"Caseins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010012","descriptor_name":"Osteogenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D010012","descriptor_name":"Osteogenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D010012","descriptor_name":"Osteogenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013422","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013422","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013422&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40880496","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40880496","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:europepmc.org:11415975","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12611171","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:20723221fdfd48e281fd0d80b4ac5480","is_oa":true,"landing_page_url":"https://doaj.org/article/20723221fdfd48e281fd0d80b4ac5480","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 8, p e1013422 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013422","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013422","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013422&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413847180.pdf","grobid_xml":"https://content.openalex.org/works/W4413847180.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W2051627306","https://openalex.org/W2060592857","https://openalex.org/W2064720410","https://openalex.org/W2066622802","https://openalex.org/W2072407000","https://openalex.org/W2077847043","https://openalex.org/W2099153308","https://openalex.org/W2138216052","https://openalex.org/W2193844257","https://openalex.org/W2344689512","https://openalex.org/W2593500554","https://openalex.org/W2789857505","https://openalex.org/W2799876761","https://openalex.org/W3091783376","https://openalex.org/W3112376646","https://openalex.org/W3154128579","https://openalex.org/W3177500196","https://openalex.org/W3187526345","https://openalex.org/W3199607358","https://openalex.org/W4200203717","https://openalex.org/W4223507828","https://openalex.org/W4226068113","https://openalex.org/W4229056282","https://openalex.org/W4244736178","https://openalex.org/W4283516025","https://openalex.org/W4286462353","https://openalex.org/W4286500588","https://openalex.org/W4298127656","https://openalex.org/W4303453384","https://openalex.org/W4306850125","https://openalex.org/W4308834846","https://openalex.org/W4309737076","https://openalex.org/W4310255070","https://openalex.org/W4312866390","https://openalex.org/W4319455258","https://openalex.org/W4321498129","https://openalex.org/W4323967728","https://openalex.org/W4376621536","https://openalex.org/W4377142604","https://openalex.org/W4386590253","https://openalex.org/W4387491415","https://openalex.org/W4389312755","https://openalex.org/W4390474323","https://openalex.org/W4391311472","https://openalex.org/W4391884307","https://openalex.org/W4392638831","https://openalex.org/W4392937438","https://openalex.org/W4394573404","https://openalex.org/W4399066674","https://openalex.org/W4399172600","https://openalex.org/W4399276062","https://openalex.org/W4399303421","https://openalex.org/W4400256024","https://openalex.org/W4402949285"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Bone":[0],"health":[1],"is":[2,103,112,128,140],"a":[3,16,27,46,56,82,110,131],"growing":[4],"concern":[5],"in":[6,12,65,142],"aging":[7],"populations,":[8],"and":[9,90,109],"bioactive":[10],"peptides":[11,32,60],"dairy":[13],"products":[14],"offer":[15],"promising":[17],"approach":[18],"to":[19,114],"preventing":[20],"bone-related":[21],"diseases.":[22],"However,":[23],"the":[24,36,73],"lack":[25],"of":[26,50,76],"public":[28,48],"database":[29,49,139],"for":[30,118,134],"osteogenic":[31,51],"(OPs)":[33],"has":[34],"limited":[35,74],"computational":[37],"detection":[38],"efforts.":[39],"In":[40],"this":[41],"work,":[42],"we":[43,79],"introduce":[44],"OP-AND,":[45],"curated":[47],"peptides.":[52],"We":[53],"also":[54],"propose":[55],"novel":[57],"hypothesis":[58],"that":[59,86],"derived":[61],"from":[62],"proteins":[63],"involved":[64],"osteoclast":[66],"formation":[67],"may":[68],"serve":[69],"as":[70,130],"non-osteogenic.":[71],"Considering":[72],"availability":[75],"OP":[77],"data,":[78],"present":[80],"SimPep,":[81],"deep":[83],"learning":[84],"framework":[85],"achieves":[87],"86.87%":[88],"accuracy":[89],"76.88%":[91],"area":[92],"under":[93],"receiver-operating":[94],"characteristic":[95],"curve":[96],"score":[97],"using":[98],"five-fold":[99],"cross-validation.":[100],"SimPep's":[101],"performance":[102],"further":[104],"evaluated":[105],"on":[106],"external":[107],"datasets,":[108],"pipeline":[111],"introduced":[113],"select":[115],"potential":[116],"OPs":[117],"experimental":[119],"studies.":[120],"The":[121,137],"camel":[122],"milk":[123],"alpha":[124],"s1-casein":[125],"peptide":[126],"'MKLLILTCLVAVALARPKYPLRYPEVF'":[127],"highlighted":[129],"top":[132],"candidate":[133],"future":[135],"exploration.":[136],"OP-AND":[138],"available":[141],"https://github.com/CBRC-lab/SimPep_and_OP-AND.":[143]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-08-19T15:00:24.278416","created_date":"2025-10-10T00:00:00"}
