{"id":"https://openalex.org/W4387346479","doi":"https://doi.org/10.1145/3584371.3613007","title":"AcrTransAct: Pre-trained Protein Transformer Models for the Detection of Type I Anti-CRISPR Activities","display_name":"AcrTransAct: Pre-trained Protein Transformer Models for the Detection of Type I Anti-CRISPR Activities","publication_year":2023,"publication_date":"2023-09-03","ids":{"openalex":"https://openalex.org/W4387346479","doi":"https://doi.org/10.1145/3584371.3613007"},"language":"en","primary_location":{"id":"doi:10.1145/3584371.3613007","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3613007","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613007","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613007","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055158775","display_name":"Moein Hasani","orcid":"https://orcid.org/0009-0009-4117-4289"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Moein Hasani","raw_affiliation_strings":["Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada"],"raw_orcid":"https://orcid.org/0009-0009-4117-4289","affiliations":[{"raw_affiliation_string":"Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063584593","display_name":"Chantel N. Trost","orcid":"https://orcid.org/0000-0002-6782-2143"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chantel N. Trost","raw_affiliation_strings":["Molecular Genetics, University of Toronto, Toronto, Ontario, Canada"],"raw_orcid":"https://orcid.org/0000-0002-6782-2143","affiliations":[{"raw_affiliation_string":"Molecular Genetics, University of Toronto, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093003484","display_name":"Nolen J. Timmerman","orcid":"https://orcid.org/0009-0000-8531-855X"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nolen Timmerman","raw_affiliation_strings":["Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada"],"raw_orcid":"https://orcid.org/0009-0000-8531-855X","affiliations":[{"raw_affiliation_string":"Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089050646","display_name":"Lingling Jin","orcid":"https://orcid.org/0000-0002-4586-2347"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lingling Jin","raw_affiliation_strings":["Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada"],"raw_orcid":"https://orcid.org/0000-0002-4586-2347","affiliations":[{"raw_affiliation_string":"Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada","institution_ids":["https://openalex.org/I32625721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5055158775"],"corresponding_institution_ids":["https://openalex.org/I32625721"],"apc_list":null,"apc_paid":null,"fwci":0.7497,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73085434,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":1.0,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9894000291824341,"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/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.9843000173568726,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.972545325756073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6427634358406067},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.579138457775116},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5613692998886108},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5231505632400513},{"id":"https://openalex.org/keywords/palindrome","display_name":"Palindrome","score":0.4914954900741577},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42414456605911255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38494783639907837},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29574573040008545},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23128733038902283},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.21518096327781677}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.972545325756073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6427634358406067},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.579138457775116},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5613692998886108},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5231505632400513},{"id":"https://openalex.org/C44667518","wikidata":"https://www.wikidata.org/wiki/Q12321","display_name":"Palindrome","level":4,"score":0.4914954900741577},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42414456605911255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38494783639907837},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29574573040008545},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23128733038902283},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.21518096327781677},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3584371.3613007","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3613007","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613007","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3584371.3613007","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3613007","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3613007","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1799814265","display_name":null,"funder_award_id":"RGPIN-2019-06424","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387346479.pdf","grobid_xml":"https://content.openalex.org/works/W4387346479.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2045435533","https://openalex.org/W2076048958","https://openalex.org/W2101503754","https://openalex.org/W2174616186","https://openalex.org/W2430331709","https://openalex.org/W2601226883","https://openalex.org/W2621096268","https://openalex.org/W2757079914","https://openalex.org/W2764223254","https://openalex.org/W2995081665","https://openalex.org/W3096574358","https://openalex.org/W3097237310","https://openalex.org/W3126278067","https://openalex.org/W3177500196","https://openalex.org/W3199468887","https://openalex.org/W4206389846","https://openalex.org/W4206993365","https://openalex.org/W4210702584","https://openalex.org/W4249942339","https://openalex.org/W4280612257","https://openalex.org/W4281993476","https://openalex.org/W4327550249"],"related_works":["https://openalex.org/W4256679810","https://openalex.org/W2940472313","https://openalex.org/W2004311938","https://openalex.org/W2091512593","https://openalex.org/W2950606817","https://openalex.org/W4365999895","https://openalex.org/W2978271661","https://openalex.org/W1966021055","https://openalex.org/W4232796816","https://openalex.org/W2990696275"],"abstract_inverted_index":{"Clustered":[0],"Regularly":[1],"Interspaced":[2],"Short":[3],"Palindromic":[4],"Repeats":[5],"(CRISPR)":[6],"and":[7,29,43,77,96,164,199,212,223,236,276],"CRISPR-associated":[8],"(Cas)":[9],"proteins":[10,38,50,67],"serve":[11],"as":[12],"a":[13,54,129,150,156,172,179,270],"formidable":[14],"defense":[15],"mechanism":[16],"for":[17,104],"bacteria":[18,60],"against":[19],"foreign":[20],"DNA;":[21],"on":[22,214],"the":[23,59,73,118,137,165,231,254,262],"other":[24,30],"hand,":[25],"some":[26],"bacteriophages":[27],"(phages)":[28],"mobile":[31],"genetic":[32],"elements":[33],"have":[34],"evolved":[35],"anti-CRISPR":[36],"(Acr)":[37],"to":[39,58,75,82,85,111,135,260],"counteract":[40],"CRISPR-Cas":[41,70,141,238,266],"systems":[42,71,239,267],"ensure":[44],"their":[45],"own":[46],"survival.":[47],"Because":[48],"Acr":[49,66,90,193,272],"provide":[51],"phages":[52,84],"with":[53,253],"fitness":[55],"advantage":[56],"relative":[57],"that":[61,68,154,175],"they":[62],"infect,":[63],"accurately":[64],"identifying":[65],"inhibit":[69],"has":[72],"potential":[74],"significantly":[76],"positively":[78],"impact":[79],"our":[80,243],"ability":[81],"harness":[83],"fight":[86],"antimicrobial":[87],"resistance.":[88],"However,":[89],"identification":[91],"is,":[92],"at":[93],"present,":[94],"laborious":[95],"involves":[97],"costly":[98],"experimental":[99],"procedures.":[100],"Existing":[101],"computational":[102],"tools":[103],"protein-protein":[105],"interaction":[106],"(PPI)":[107],"are":[108,278],"not":[109],"designed":[110],"predict":[112,136,261],"complex":[113],"inhibition,":[114],"which":[115],"could":[116],"be":[117],"collective":[119],"result":[120],"of":[121,139,177,221,227,233,248,264],"multiple":[122,265],"PPIs.":[123],"In":[124],"this":[125,215,258],"study,":[126],"we":[127],"developed":[128],"transformer-based":[130],"deep":[131],"neural":[132,183],"network,":[133],"AcrTransAct,":[134],"probability":[138,263],"Acr-mediated":[140],"inhibition.":[142],"Our":[143,274],"model":[144,209],"comprises":[145],"two":[146,192],"main":[147],"components:":[148],"1.":[149],"feature":[151],"extraction":[152],"module":[153,174],"incorporates":[155],"pre-trained":[157],"Evolutionary":[158],"Scale":[159],"Modeling":[160],"(ESM)":[161],"protein":[162],"transformer":[163],"NetSurfP-3.0":[166],"secondary":[167],"structure":[168],"prediction":[169],"system;":[170],"2.":[171],"classification":[173],"consists":[176],"either":[178],"convolutional":[180],"or":[181],"recurrent":[182],"network.":[184],"We":[185,217],"created":[186],"an":[187,219,224],"inhibition":[188,232],"dataset":[189],"compiled":[190],"from":[191,257],"databases,":[194],"AcrHub":[195],"[30],":[196],"Anti-CRISPRdb":[197],"[5],":[198],"several":[200],"published":[201],"works":[202],"[9,":[203],"12,":[204],"18,":[205],"20].":[206],"The":[207],"AcrTransAct":[208,249],"is":[210,251],"trained":[211],"tested":[213],"dataset.":[216,244],"achieved":[218],"accuracy":[220],"95%":[222],"F1":[225],"score":[226],"0.95":[228],"in":[229,242],"predicting":[230],"I-C,":[234],"I-E,":[235],"I-F":[237],"by":[240,269],"Acrs":[241],"A":[245],"web":[246],"application":[247],"(https://acrtransact.usask.ca)":[250],"implemented":[252],"best-performing":[255],"models":[256],"study":[259],"inhibited":[268],"putative":[271],"protein.":[273],"code":[275],"data":[277],"available":[279],"here:":[280],"https://github.com/USask-BINFO/AcrTransAct.":[281]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
