{"id":"https://openalex.org/W4226068113","doi":"https://doi.org/10.1093/bib/bbac174","title":"ToxinPred2: an improved method for predicting toxicity of proteins","display_name":"ToxinPred2: an improved method for predicting toxicity of proteins","publication_year":2022,"publication_date":"2022-04-20","ids":{"openalex":"https://openalex.org/W4226068113","doi":"https://doi.org/10.1093/bib/bbac174","pmid":"https://pubmed.ncbi.nlm.nih.gov/35595541"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac174","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac174","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://github.com/raghavagps/toxinpred2/tree/v1.0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101954612","display_name":"Neelam Sharma","orcid":"https://orcid.org/0000-0002-1765-3644"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Neelam Sharma","raw_affiliation_strings":["Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India"],"raw_orcid":"https://orcid.org/0000-0002-1765-3644","affiliations":[{"raw_affiliation_string":"Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":[]},{"raw_affiliation_string":"Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":["https://openalex.org/I119939252"]},{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022895624","display_name":"Leimarembi Devi Naorem","orcid":"https://orcid.org/0000-0002-2454-2862"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Leimarembi Devi Naorem","raw_affiliation_strings":["Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India"],"raw_orcid":"https://orcid.org/0000-0002-2454-2862","affiliations":[{"raw_affiliation_string":"Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":[]},{"raw_affiliation_string":"Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":["https://openalex.org/I119939252"]},{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046619508","display_name":"Shipra Jain","orcid":"https://orcid.org/0000-0002-7045-5188"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Shipra Jain","raw_affiliation_strings":["Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India"],"raw_orcid":"https://orcid.org/0000-0002-7045-5188","affiliations":[{"raw_affiliation_string":"Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":[]},{"raw_affiliation_string":"Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":["https://openalex.org/I119939252"]},{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051938893","display_name":"Gajendra P. S. Raghava","orcid":"https://orcid.org/0000-0002-8902-2876"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Gajendra P S Raghava","raw_affiliation_strings":["Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India"],"raw_orcid":"https://orcid.org/0000-0002-8902-2876","affiliations":[{"raw_affiliation_string":"Department of Computational Biology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":[]},{"raw_affiliation_string":"Indraprastha Institute of Information Technology , , Okhla Phase 3, New Delhi-110020 , India","institution_ids":["https://openalex.org/I119939252"]},{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5051938893"],"corresponding_institution_ids":["https://openalex.org/I119939252"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":24.5119,"has_fulltext":false,"cited_by_count":335,"citation_normalized_percentile":{"value":0.99812533,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9987000226974487,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9987000226974487,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9943000078201294,"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":0.9912999868392944,"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":0.7104529142379761},{"id":"https://openalex.org/keywords/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.6661144495010376},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5238642692565918},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.45518913865089417},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4344043731689453},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4052683115005493},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.16578781604766846}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7104529142379761},{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.6661144495010376},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5238642692565918},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.45518913865089417},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4344043731689453},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4052683115005493},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.16578781604766846},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000633","qualifier_name":"toxicity","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000633","qualifier_name":"toxicity","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000633","qualifier_name":"toxicity","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbac174","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac174","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35595541","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35595541","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:doi:10.5281/zenodo.19884497","is_oa":true,"landing_page_url":"https://github.com/raghavagps/toxinpred2/tree/v1.0","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.19884497","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.19884497","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"},{"id":"doi:10.5281/zenodo.19884498","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.19884498","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:doi:10.5281/zenodo.19884497","is_oa":true,"landing_page_url":"https://github.com/raghavagps/toxinpred2/tree/v1.0","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1990075477","https://openalex.org/W1992450378","https://openalex.org/W2010688088","https://openalex.org/W2012990453","https://openalex.org/W2014274241","https://openalex.org/W2030623877","https://openalex.org/W2039516884","https://openalex.org/W2044573804","https://openalex.org/W2048211729","https://openalex.org/W2055043387","https://openalex.org/W2056132907","https://openalex.org/W2101005439","https://openalex.org/W2101234009","https://openalex.org/W2102023232","https://openalex.org/W2109598625","https://openalex.org/W2156125289","https://openalex.org/W2158714788","https://openalex.org/W2160227697","https://openalex.org/W2161716000","https://openalex.org/W2189911347","https://openalex.org/W2295598076","https://openalex.org/W2322844633","https://openalex.org/W2492513888","https://openalex.org/W2530149620","https://openalex.org/W2589065420","https://openalex.org/W2589845476","https://openalex.org/W2739980134","https://openalex.org/W2768348081","https://openalex.org/W2770630458","https://openalex.org/W2791066888","https://openalex.org/W2801088198","https://openalex.org/W2884499161","https://openalex.org/W2910110288","https://openalex.org/W2918544128","https://openalex.org/W2933605448","https://openalex.org/W2944360550","https://openalex.org/W2990887264","https://openalex.org/W3009548091","https://openalex.org/W3036119229","https://openalex.org/W3044326329","https://openalex.org/W3048086963","https://openalex.org/W3088621177","https://openalex.org/W3094373383","https://openalex.org/W3101256226","https://openalex.org/W3112376646","https://openalex.org/W3127020663","https://openalex.org/W3145990216","https://openalex.org/W3189511324","https://openalex.org/W4206722897","https://openalex.org/W4213149192","https://openalex.org/W6675354045","https://openalex.org/W6683614669","https://openalex.org/W6684097780","https://openalex.org/W6745609711","https://openalex.org/W6761383852"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4313488044","https://openalex.org/W3209574120","https://openalex.org/W4312192474","https://openalex.org/W4210805261"],"abstract_inverted_index":{"Proteins/peptides":[0],"have":[1,96,199],"shown":[2],"to":[3],"be":[4],"promising":[5],"therapeutic":[6],"agents":[7],"for":[8,32,46,101,225],"a":[9,27,128,155,165,214,221],"variety":[10],"of":[11,17,36,42,49,70,83,93,131,229,232,235],"diseases.":[12],"However,":[13],"toxicity":[14,35,48,228],"is":[15,39,209,220],"one":[16],"the":[18,34,67,71,84,90,98,181,203,227],"obstacles":[19],"in":[20,202],"protein/peptide-based":[21],"therapy.":[22],"The":[23,54,194],"current":[24],"study":[25],"describes":[26],"web-based":[28],"tool,":[29],"ToxinPred2,":[30],"developed":[31,44,154,187,224],"predicting":[33,47,102,226],"proteins.":[37,53],"This":[38,219],"an":[40],"update":[41],"ToxinPred":[43],"mainly":[45],"peptides":[50],"and":[51,60,86,114,119,124,146,163,191,213],"small":[52],"method":[55,157,223],"has":[56],"been":[57,200],"trained,":[58],"tested":[59],"evaluated":[61],"on":[62,81,89,140,180,189],"three":[63,161],"datasets":[64],"curated":[65],"from":[66],"recent":[68],"release":[69],"SwissProt.":[72],"To":[73],"provide":[74],"unbiased":[75],"evaluation,":[76],"we":[77,153,186],"performed":[78],"internal":[79],"validation":[80,88,182],"80%":[82],"data":[85],"external":[87],"remaining":[91],"20%":[92],"data.":[94],"We":[95],"implemented":[97,201],"following":[99],"techniques":[100,126,142],"protein":[103],"toxicity;":[104],"(i)":[105],"Basic":[106],"Local":[107],"Alignment":[108],"Search":[109],"Tool-based":[110],"similarity,":[111],"(ii)":[112],"Motif-EmeRging":[113],"with":[115,134,148,175],"Classes-Identification-based":[116],"motif":[117],"search":[118],"(iii)":[120],"Prediction":[121],"models.":[122],"Similarity":[123],"motif-based":[125],"achieved":[127,143,164],"high":[129,150],"probability":[130],"correct":[132],"prediction":[133],"poor":[135],"sensitivity/coverage,":[136],"whereas":[137],"models":[138,188,198],"based":[139],"machine-learning":[141],"balance":[144],"sensitivity":[145],"specificity":[147],"reasonably":[149],"accuracy.":[151],"Finally,":[152],"hybrid":[156],"that":[158],"combined":[159],"all":[160],"approaches":[162],"maximum":[166],"area":[167],"under":[168],"receiver":[169],"operating":[170],"characteristic":[171],"curve":[172],"around":[173],"0.99":[174],"Matthews":[176],"correlation":[177],"coefficient":[178],"0.91":[179],"dataset.":[183],"In":[184],"addition,":[185],"alternate":[190],"realistic":[192],"datasets.":[193],"best":[195],"machine":[196],"learning":[197],"web":[204],"server":[205],"named":[206],"'ToxinPred2',":[207],"which":[208],"available":[210],"at":[211,217],"https://webs.iiitd.edu.in/raghava/toxinpred2/":[212],"standalone":[215],"version":[216],"https://github.com/raghavagps/toxinpred2.":[218],"general":[222],"proteins":[230],"regardless":[231],"their":[233],"source":[234],"origin.":[236]},"counts_by_year":[{"year":2026,"cited_by_count":53},{"year":2025,"cited_by_count":129},{"year":2024,"cited_by_count":104},{"year":2023,"cited_by_count":36},{"year":2022,"cited_by_count":12}],"updated_date":"2026-06-18T10:00:31.954636","created_date":"2025-10-10T00:00:00"}
