{"id":"https://openalex.org/W4401328222","doi":"https://doi.org/10.1371/journal.pcbi.1011831","title":"DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models","display_name":"DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models","publication_year":2024,"publication_date":"2024-08-05","ids":{"openalex":"https://openalex.org/W4401328222","doi":"https://doi.org/10.1371/journal.pcbi.1011831","pmid":"https://pubmed.ncbi.nlm.nih.gov/39102416"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011831","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011831","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1011831","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093126855","display_name":"Robby Concha-Eloko","orcid":"https://orcid.org/0009-0000-5646-0055"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Robby Concha-Eloko","raw_affiliation_strings":["Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain"],"affiliations":[{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079406761","display_name":"Michiel Stock","orcid":"https://orcid.org/0000-0003-0903-6061"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Michiel Stock","raw_affiliation_strings":["KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012437460","display_name":"Bernard De Baets","orcid":"https://orcid.org/0000-0002-3876-620X"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Bernard De Baets","raw_affiliation_strings":["KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056367492","display_name":"Yves Briers","orcid":"https://orcid.org/0000-0001-7723-1040"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Yves Briers","raw_affiliation_strings":["Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035909668","display_name":"Rafael Sanju\u00e1n","orcid":"https://orcid.org/0000-0002-1844-545X"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Rafael Sanju\u00e1n","raw_affiliation_strings":["Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain"],"affiliations":[{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065792523","display_name":"Pilar Domingo\u2010Calap","orcid":"https://orcid.org/0000-0003-2829-8809"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Pilar Domingo-Calap","raw_affiliation_strings":["Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain"],"affiliations":[{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087430694","display_name":"Dimitri Boeckaerts","orcid":"https://orcid.org/0000-0002-7668-2840"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Dimitri Boeckaerts","raw_affiliation_strings":["KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium","Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium"],"affiliations":[{"raw_affiliation_string":"KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5012437460","https://openalex.org/A5035909668","https://openalex.org/A5056367492","https://openalex.org/A5065792523","https://openalex.org/A5079406761","https://openalex.org/A5087430694","https://openalex.org/A5093126855"],"corresponding_institution_ids":["https://openalex.org/I16097986","https://openalex.org/I32597200","https://openalex.org/I4210152685"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":12.5791,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.99029358,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"20","issue":"8","first_page":"e1011831","last_page":"e1011831"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9954000115394592,"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":0.9833999872207642,"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/annotation","display_name":"Annotation","score":0.7084757685661316},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6813972592353821},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6109044551849365},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.603364109992981},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5740998387336731},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5433031916618347},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5145518183708191},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.48782065510749817},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4577570855617523},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45677393674850464},{"id":"https://openalex.org/keywords/phage-display","display_name":"Phage display","score":0.45652735233306885},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4297764301300049},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3382641077041626},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17964407801628113},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11333364248275757}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7084757685661316},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6813972592353821},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6109044551849365},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.603364109992981},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5740998387336731},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5433031916618347},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5145518183708191},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.48782065510749817},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4577570855617523},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45677393674850464},{"id":"https://openalex.org/C186268636","wikidata":"https://www.wikidata.org/wiki/Q896217","display_name":"Phage display","level":3,"score":0.45652735233306885},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4297764301300049},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3382641077041626},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17964407801628113},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11333364248275757},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.0},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002265","descriptor_name":"Carboxylic Ester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011831","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011831","pdf_url":null,"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:39102416","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39102416","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:archive.ugent.be:01J5MNHRKRMQFSVFWFK7EBP2WF","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-01J5MNHRKRMQFSVFWFK7EBP2WF","pdf_url":"https://biblio.ugent.be/publication/01J5MNHRKRMQFSVFWFK7EBP2WF/file/01J5MNNK4VQZ002GMNSCVCYRS7.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"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":"ISSN: 1553-7358","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:11326577","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11326577","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11326577/pdf/pcbi.1011831.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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:61803d79c692467394b6e96331a014e4","is_oa":true,"landing_page_url":"https://doaj.org/article/61803d79c692467394b6e96331a014e4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 8, p e1011831 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011831","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011831","pdf_url":null,"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":[{"id":"https://openalex.org/G1320060331","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/50110001103","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G1422035950","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"},{"id":"https://openalex.org/G1598597440","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/5011000110","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G1643949827","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G1714292816","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"},{"id":"https://openalex.org/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2729857623","display_name":null,"funder_award_id":"RYC2019-028015-I","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2969783435","display_name":null,"funder_award_id":"CIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G300979063","display_name":null,"funder_award_id":"10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3219925899","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3429648993","display_name":null,"funder_award_id":"PID202","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3815942919","display_name":null,"funder_award_id":"Onderzoeksprogramma Artici\u00eble Intelligentie (AI) Vlaanderen","funder_id":"https://openalex.org/F4320321587","funder_display_name":"Vlaamse Overheid"},{"id":"https://openalex.org/G4115436907","display_name":null,"funder_award_id":"MCIN/AEI /10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4126322094","display_name":null,"funder_award_id":"01100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4305436266","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G4899110358","display_name":null,"funder_award_id":"PID2020-112835RA-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5080475149","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5318822575","display_name":null,"funder_award_id":"SEJIGENT/2021/014","funder_id":"https://openalex.org/F4320336489","funder_display_name":"Conselleria de Innovaci\u00f3n, Universidades, Ciencia y Sociedad Digital, Generalitat Valenciana"},{"id":"https://openalex.org/G5388806002","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5559701437","display_name":null,"funder_award_id":"MCIN/AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320320916","funder_display_name":"European Society of Clinical Microbiology and Infectious Diseases"},{"id":"https://openalex.org/G5711856125","display_name":null,"funder_award_id":"20200063","funder_id":"https://openalex.org/F4320320916","funder_display_name":"European Society of Clinical Microbiology and Infectious Diseases"},{"id":"https://openalex.org/G6218905885","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G661330594","display_name":null,"funder_award_id":"00110","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G6685425346","display_name":null,"funder_award_id":"0011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G6717538712","display_name":null,"funder_award_id":"AEI /10.13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7084143925","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7184321070","display_name":null,"funder_award_id":"GRISOLIAP/2020/158","funder_id":"https://openalex.org/F4320336489","funder_display_name":"Conselleria de Innovaci\u00f3n, Universidades, Ciencia y Sociedad Digital, Generalitat Valenciana"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7535663061","display_name":null,"funder_award_id":"AEI/10.","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8260616629","display_name":null,"funder_award_id":"011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8638682022","display_name":null,"funder_award_id":"10.13039/50110001103","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8888022036","display_name":null,"funder_award_id":"AEI/10.13039/501100011033","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G968893856","display_name":null,"funder_award_id":"1S69520N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320320916","display_name":"European Society of Clinical Microbiology and Infectious Diseases","ror":"https://ror.org/02vkssr45"},{"id":"https://openalex.org/F4320321587","display_name":"Vlaamse Overheid","ror":"https://ror.org/04qxsrb28"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320321864","display_name":"Generalitat Valenciana","ror":"https://ror.org/0097mvx21"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null},{"id":"https://openalex.org/F4320336489","display_name":"Conselleria de Innovaci\u00f3n, Universidades, Ciencia y Sociedad Digital, Generalitat Valenciana","ror":null},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W112013909","https://openalex.org/W2027005563","https://openalex.org/W2033044694","https://openalex.org/W2070300719","https://openalex.org/W2076048958","https://openalex.org/W2126587104","https://openalex.org/W2127322768","https://openalex.org/W2128007785","https://openalex.org/W2156125289","https://openalex.org/W2165232124","https://openalex.org/W2165510614","https://openalex.org/W2192991381","https://openalex.org/W2265024698","https://openalex.org/W2443992611","https://openalex.org/W2897531714","https://openalex.org/W2949676527","https://openalex.org/W2950954328","https://openalex.org/W2972411752","https://openalex.org/W2983772326","https://openalex.org/W2999406779","https://openalex.org/W3003829447","https://openalex.org/W3023787861","https://openalex.org/W3096218861","https://openalex.org/W3101667854","https://openalex.org/W3146944767","https://openalex.org/W3157992500","https://openalex.org/W3176919622","https://openalex.org/W3177500196","https://openalex.org/W3178799249","https://openalex.org/W3189053267","https://openalex.org/W3191164977","https://openalex.org/W3196095379","https://openalex.org/W3202488381","https://openalex.org/W3217216416","https://openalex.org/W4213112325","https://openalex.org/W4223644783","https://openalex.org/W4226313562","https://openalex.org/W4282946147","https://openalex.org/W4308616064","https://openalex.org/W4327550249","https://openalex.org/W4375858802","https://openalex.org/W4377091239","https://openalex.org/W4388263226","https://openalex.org/W4391316987"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2366107444","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W4388145910","https://openalex.org/W2381570729","https://openalex.org/W1533264849"],"abstract_inverted_index":{"Bacteriophages":[0],"(phages)":[1],"are":[2,29],"viruses":[3],"that":[4,45,105,121,125],"infect":[5],"bacteria.":[6],"Many":[7],"of":[8,26,132,138],"them":[9],"produce":[10],"specific":[11],"enzymes":[12],"called":[13],"depolymerases":[14,28],"to":[15,32,56,87,96],"break":[16],"down":[17],"external":[18],"polysaccharide":[19],"structures.":[20],"Accurate":[21],"annotation":[22],"and":[23,60,83,116],"domain":[24,81,118],"identification":[25],"these":[27],"challenging":[30],"due":[31],"their":[33,61],"inherent":[34],"sequence":[35],"diversity.":[36],"Hence,":[37],"we":[38,68,123],"present":[39],"DepoScope,":[40],"a":[41,47,52,70,79,89],"machine":[42],"learning":[43],"tool":[44],"combines":[46,106],"fine-tuned":[48],"ESM-2":[49],"model":[50],"with":[51,109],"convolutional":[53],"neural":[54],"network":[55],"identify":[57],"depolymerase":[58,114],"sequences":[59],"enzymatic":[62],"domains":[63],"precisely.":[64],"To":[65],"accomplish":[66],"this,":[67],"curated":[69],"dataset":[71],"from":[72],"the":[73,102,136],"INPHARED":[74],"phage":[75],"genome":[76],"database,":[77,82],"created":[78],"polysaccharide-degrading":[80],"applied":[84],"sequential":[85],"filters":[86],"construct":[88],"high-quality":[90],"dataset,":[91],"which":[92],"is":[93,101],"subsequently":[94],"used":[95],"train":[97],"DepoScope.":[98],"Our":[99],"work":[100],"first":[103],"approach":[104],"sequence-level":[107],"predictions":[108,111],"amino-acid-level":[110],"for":[112],"accurate":[113],"detection":[115],"functional":[117],"identification.":[119],"In":[120],"way,":[122],"believe":[124],"DepoScope":[126],"can":[127],"greatly":[128],"enhance":[129],"our":[130],"understanding":[131],"phage-host":[133],"interactions":[134],"at":[135],"level":[137],"depolymerases.":[139]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}