{"id":"https://openalex.org/W4413055679","doi":"https://doi.org/10.1186/s13040-025-00469-2","title":"Exo-Tox: Identifying Exotoxins from secreted bacterial proteins","display_name":"Exo-Tox: Identifying Exotoxins from secreted bacterial proteins","publication_year":2025,"publication_date":"2025-08-08","ids":{"openalex":"https://openalex.org/W4413055679","doi":"https://doi.org/10.1186/s13040-025-00469-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/40781630"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00469-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00469-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00469-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00469-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Tanja Krueger","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]},{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tanja Krueger","raw_affiliation_strings":["Department of Informatics, Unit for Bioinformatics and Computational Biology, Technical University of Munich School of Computation, Information and Technology, Boltzmannstrasse, 85748, Garching/Munich, Bavaria, Germany","Walther-Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universit\u00e4t in Munich, Goethestrasse, 80336, Munich, Bavaria, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Unit for Bioinformatics and Computational Biology, Technical University of Munich School of Computation, Information and Technology, Boltzmannstrasse, 85748, Garching/Munich, Bavaria, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Walther-Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universit\u00e4t in Munich, Goethestrasse, 80336, Munich, Bavaria, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117099337","display_name":"Damla Ayse Durmaz","orcid":"https://orcid.org/0009-0006-8693-1616"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Damla\u00a0A. Durmaz","raw_affiliation_strings":["Walther-Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universit\u00e4t in Munich, Goethestrasse, 80336, Munich, Bavaria, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Walther-Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universit\u00e4t in Munich, Goethestrasse, 80336, Munich, Bavaria, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068231578","display_name":"Luisa F. Jim\u00e9nez\u2010Soto","orcid":"https://orcid.org/0000-0001-8551-5019"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Luisa\u00a0F. Jimenez-Soto","raw_affiliation_strings":["Walther-Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universit\u00e4t in Munich, Goethestrasse, 80336, Munich, Bavaria, Germany. l.jimenez@lmu.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Walther-Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universit\u00e4t in Munich, Goethestrasse, 80336, Munich, Bavaria, Germany. l.jimenez@lmu.de","institution_ids":["https://openalex.org/I8204097"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2690,"currency":"USD","value_usd":2690},"apc_paid":{"value":2690,"currency":"USD","value_usd":2690},"fwci":0.7512,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.70174228,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"18","issue":"1","first_page":"52","last_page":"52"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.590399980545044,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.590399980545044,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.155799999833107,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.07349999994039536,"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/context","display_name":"Context (archaeology)","score":0.6769253015518188},{"id":"https://openalex.org/keywords/transferability","display_name":"Transferability","score":0.5852770805358887},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5720395445823669},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5362716317176819},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5031484961509705},{"id":"https://openalex.org/keywords/secretory-protein","display_name":"Secretory protein","score":0.4602780044078827},{"id":"https://openalex.org/keywords/microbial-toxins","display_name":"Microbial toxins","score":0.4359561800956726},{"id":"https://openalex.org/keywords/pore-forming-toxin","display_name":"Pore-forming toxin","score":0.42710548639297485},{"id":"https://openalex.org/keywords/toxin","display_name":"Toxin","score":0.4252455234527588},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3878413438796997},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.3371087312698364},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.25834593176841736},{"id":"https://openalex.org/keywords/secretion","display_name":"Secretion","score":0.18913599848747253},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1409173309803009}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6769253015518188},{"id":"https://openalex.org/C61272859","wikidata":"https://www.wikidata.org/wiki/Q7834031","display_name":"Transferability","level":3,"score":0.5852770805358887},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5720395445823669},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5362716317176819},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5031484961509705},{"id":"https://openalex.org/C156399914","wikidata":"https://www.wikidata.org/wiki/Q7444454","display_name":"Secretory protein","level":3,"score":0.4602780044078827},{"id":"https://openalex.org/C9043230","wikidata":"https://www.wikidata.org/wiki/Q262657","display_name":"Microbial toxins","level":3,"score":0.4359561800956726},{"id":"https://openalex.org/C174921431","wikidata":"https://www.wikidata.org/wiki/Q7230047","display_name":"Pore-forming toxin","level":4,"score":0.42710548639297485},{"id":"https://openalex.org/C2777367657","wikidata":"https://www.wikidata.org/wiki/Q184651","display_name":"Toxin","level":2,"score":0.4252455234527588},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3878413438796997},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.3371087312698364},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25834593176841736},{"id":"https://openalex.org/C49039625","wikidata":"https://www.wikidata.org/wiki/Q84230","display_name":"Secretion","level":2,"score":0.18913599848747253},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1409173309803009},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C140331021","wikidata":"https://www.wikidata.org/wiki/Q1868104","display_name":"Logit","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-025-00469-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00469-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00469-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:40781630","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40781630","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":"BioData mining","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12333140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12333140","pdf_url":null,"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":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:92d16b9cf5794274afd2ae25d4f6f078","is_oa":true,"landing_page_url":"https://doaj.org/article/92d16b9cf5794274afd2ae25d4f6f078","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":"BioData Mining, Vol 18, Iss 1, Pp 1-28 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00469-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00469-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00469-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G3209870182","display_name":null,"funder_award_id":"SSTDBB-16DKWN136B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323390","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413055679.pdf","grobid_xml":"https://content.openalex.org/works/W4413055679.grobid-xml"},"referenced_works_count":87,"referenced_works":["https://openalex.org/W148231546","https://openalex.org/W263208123","https://openalex.org/W1970613018","https://openalex.org/W1982597966","https://openalex.org/W1990075477","https://openalex.org/W2001335546","https://openalex.org/W2014274241","https://openalex.org/W2043522409","https://openalex.org/W2055043387","https://openalex.org/W2096525273","https://openalex.org/W2102122585","https://openalex.org/W2123179625","https://openalex.org/W2132292391","https://openalex.org/W2135511693","https://openalex.org/W2138122982","https://openalex.org/W2158714788","https://openalex.org/W2159277024","https://openalex.org/W2160227697","https://openalex.org/W2161716000","https://openalex.org/W2162792752","https://openalex.org/W2213211970","https://openalex.org/W2294611355","https://openalex.org/W2480809770","https://openalex.org/W2488719483","https://openalex.org/W2519505900","https://openalex.org/W2530149620","https://openalex.org/W2594385802","https://openalex.org/W2620760558","https://openalex.org/W2753247802","https://openalex.org/W2793977884","https://openalex.org/W2888636777","https://openalex.org/W2900779023","https://openalex.org/W2907594772","https://openalex.org/W2943320595","https://openalex.org/W2944360550","https://openalex.org/W2950954328","https://openalex.org/W2982586313","https://openalex.org/W2995514860","https://openalex.org/W3011565753","https://openalex.org/W3012799415","https://openalex.org/W3017143673","https://openalex.org/W3044326329","https://openalex.org/W3049692992","https://openalex.org/W3092264786","https://openalex.org/W3096218861","https://openalex.org/W3104877281","https://openalex.org/W3110914504","https://openalex.org/W3122343194","https://openalex.org/W3124620674","https://openalex.org/W3126232929","https://openalex.org/W3131565611","https://openalex.org/W3145990216","https://openalex.org/W3146944767","https://openalex.org/W3164126481","https://openalex.org/W3173561065","https://openalex.org/W3177500196","https://openalex.org/W3202005026","https://openalex.org/W4205192056","https://openalex.org/W4205440119","https://openalex.org/W4205773061","https://openalex.org/W4206722897","https://openalex.org/W4206950245","https://openalex.org/W4220799031","https://openalex.org/W4225460848","https://openalex.org/W4225891318","https://openalex.org/W4226068113","https://openalex.org/W4281291878","https://openalex.org/W4289274885","https://openalex.org/W4293770948","https://openalex.org/W4307645443","https://openalex.org/W4318480056","https://openalex.org/W4324304780","https://openalex.org/W4375858802","https://openalex.org/W4385954015","https://openalex.org/W4390706033","https://openalex.org/W4392344527","https://openalex.org/W4394756259","https://openalex.org/W4398173116","https://openalex.org/W4400864148","https://openalex.org/W4401086300","https://openalex.org/W4401728757","https://openalex.org/W4402278817","https://openalex.org/W4404282005","https://openalex.org/W4409154153","https://openalex.org/W4410545719","https://openalex.org/W4410799875","https://openalex.org/W4411327286"],"related_works":["https://openalex.org/W2154546942","https://openalex.org/W2022324929","https://openalex.org/W762037996","https://openalex.org/W2371336165","https://openalex.org/W1568452228","https://openalex.org/W289016260","https://openalex.org/W4251831847","https://openalex.org/W1997136952","https://openalex.org/W3090774041","https://openalex.org/W2033053808"],"abstract_inverted_index":{"BACKGROUND:":[0],"Bacterial":[1],"exotoxins":[2,98],"are":[3,189],"secreted":[4,100],"proteins":[5,158],"able":[6],"to":[7,69,112,156,198],"affect":[8],"target":[9],"cells,":[10],"and":[11,22,44,78,99,120,159,184,203],"associated":[12],"with":[13],"diseases.":[14],"Their":[15],"accurate":[16,192],"identification":[17],"can":[18],"enhance":[19],"drug":[20],"discovery":[21],"ensure":[23],"the":[24,146,178,199,207],"safety":[25],"of":[26,96,142,148,180],"bacteria-based":[27],"medical":[28],"applications.":[29],"However,":[30],"current":[31],"toxin":[32,71,122],"predictors":[33,188],"prioritize":[34],"broad":[35],"coverage":[36],"by":[37,73,107,172],"mixing":[38],"toxins":[39],"from":[40,81],"multiple":[41,127],"biological":[42],"kingdoms":[43],"diverse":[45],"control":[46],"sets.":[47],"This":[48],"general":[49],"approach":[50],"has":[51],"proven":[52],"sub-optimal":[53],"for":[54,191],"identifying":[55],"niche":[56,170],"toxins,":[57],"such":[58],"as":[59,105],"bacterial":[60,97,102,166],"exotoxins.":[61],"Recent":[62],"Protein":[63,108],"Language":[64,109],"Models":[65],"offer":[66],"an":[67],"opportunity":[68],"improve":[70],"prediction":[72],"capturing":[74],"global":[75],"sequence":[76],"context":[77],"biochemical":[79],"properties":[80],"protein":[82,143],"sequences.":[83],"RESULTS:":[84],"We":[85,151,194],"introduce":[86],"Exo-Tox,":[87],"a":[88,130,169],"specialized":[89,187],"predictor":[90],"trained":[91],"exclusively":[92],"on":[93],"curated":[94],"datasets":[95],"non-toxic":[101],"proteins,":[103],"represented":[104],"embeddings":[106],"Models.":[110],"Compared":[111],"Basic":[113],"Local":[114],"Alignment":[115],"Search":[116],"Tool":[117],"(BLAST)-based":[118],"methods":[119],"generalized":[121,173],"predictors,":[123],"Exo-Tox":[124,163],"outperforms":[125],"across":[126],"metrics,":[128],"achieving":[129],"Matthews":[131],"correlation":[132],"coefficient":[133],">":[134],"0.9.":[135],"Notably,":[136],"Exo-Tox's":[137],"performance":[138],"remains":[139],"robust":[140],"regardless":[141],"length":[144],"or":[145],"presence":[147],"signal":[149],"peptides.":[150],"analyze":[152],"its":[153],"limited":[154],"transferability":[155],"bacteriophage":[157],"non-secreted":[160],"proteins.":[161],"CONCLUSION:":[162],"reliably":[164],"identifies":[165],"exotoxins,":[167],"filling":[168],"overlooked":[171],"predictors.":[174],"Our":[175],"findings":[176],"highlight":[177],"importance":[179],"domain-specific":[181],"training":[182,201],"data":[183],"emphasize":[185],"that":[186],"necessary":[190],"classification.":[193],"provide":[195],"open":[196],"access":[197],"model,":[200],"data,":[202],"usage":[204],"guidelines":[205],"via":[206],"LMU":[208],"Munich":[209],"Open":[210],"Data":[211],"repository.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}
