{"id":"https://openalex.org/W2971253990","doi":"https://doi.org/10.1093/bioinformatics/btz670","title":"ChaperISM: improved chaperone binding prediction using position-independent scoring matrices","display_name":"ChaperISM: improved chaperone binding prediction using position-independent scoring matrices","publication_year":2019,"publication_date":"2019-08-27","ids":{"openalex":"https://openalex.org/W2971253990","doi":"https://doi.org/10.1093/bioinformatics/btz670","mag":"2971253990","pmid":"https://pubmed.ncbi.nlm.nih.gov/31504177"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz670","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz670","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/735/32369857/btz670.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/735/32369857/btz670.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035468408","display_name":"M B B Gutierres","orcid":null},"institutions":[{"id":"https://openalex.org/I134363262","display_name":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre","ror":"https://ror.org/00x0nkm13","country_code":"BR","type":"education","lineage":["https://openalex.org/I134363262"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"M B B Gutierres","raw_affiliation_strings":["Laborat\u00f3rio de Imunoterapia, Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre , Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Imunoterapia, Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre , Porto Alegre, Brazil","institution_ids":["https://openalex.org/I134363262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042204528","display_name":"Cristina Bonorino","orcid":"https://orcid.org/0000-0003-2755-3978"},"institutions":[{"id":"https://openalex.org/I134363262","display_name":"Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre","ror":"https://ror.org/00x0nkm13","country_code":"BR","type":"education","lineage":["https://openalex.org/I134363262"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"C B C Bonorino","raw_affiliation_strings":["Laborat\u00f3rio de Imunoterapia, Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre , Porto Alegre, Brazil","School of Medicine, Department of Surgery, University of California San Diego , La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Imunoterapia, Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre , Porto Alegre, Brazil","institution_ids":["https://openalex.org/I134363262"]},{"raw_affiliation_string":"School of Medicine, Department of Surgery, University of California San Diego , La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034774826","display_name":"Maur\u00edcio Rigo","orcid":"https://orcid.org/0000-0002-1584-6194"},"institutions":[{"id":"https://openalex.org/I45643870","display_name":"Pontif\u00edcia Universidade Cat\u00f3lica do Rio Grande do Sul","ror":"https://ror.org/025vmq686","country_code":"BR","type":"education","lineage":["https://openalex.org/I45643870"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"M M Rigo","raw_affiliation_strings":["Escola de Medicina, Laborat\u00f3rio de Imunologia Cl\u00ednica e Experimental, Pontif\u00edcia Universidade Cat\u00f3lica do Rio Grande do Sul , Porto Alegre, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Escola de Medicina, Laborat\u00f3rio de Imunologia Cl\u00ednica e Experimental, Pontif\u00edcia Universidade Cat\u00f3lica do Rio Grande do Sul , Porto Alegre, Brazil","institution_ids":["https://openalex.org/I45643870"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5034774826"],"corresponding_institution_ids":["https://openalex.org/I45643870"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3662,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.81121906,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"3","first_page":"735","last_page":"741"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10934","display_name":"Heat shock proteins research","score":0.8948000073432922,"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/T10934","display_name":"Heat shock proteins research","score":0.8948000073432922,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.049300000071525574,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.014399999752640724,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6280955672264099},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6000061631202698},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5808870792388916},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.547293484210968},{"id":"https://openalex.org/keywords/chaperone","display_name":"Chaperone (clinical)","score":0.5194982290267944},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48929354548454285},{"id":"https://openalex.org/keywords/hsp70","display_name":"Hsp70","score":0.4543962776660919},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.41813600063323975},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37642163038253784},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3707122802734375},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3247360587120056},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23238754272460938},{"id":"https://openalex.org/keywords/heat-shock-protein","display_name":"Heat shock protein","score":0.23236781358718872},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1464838683605194}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6280955672264099},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6000061631202698},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5808870792388916},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.547293484210968},{"id":"https://openalex.org/C2775962898","wikidata":"https://www.wikidata.org/wiki/Q5073152","display_name":"Chaperone (clinical)","level":2,"score":0.5194982290267944},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48929354548454285},{"id":"https://openalex.org/C68991219","wikidata":"https://www.wikidata.org/wiki/Q419102","display_name":"Hsp70","level":4,"score":0.4543962776660919},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.41813600063323975},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37642163038253784},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3707122802734375},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3247360587120056},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23238754272460938},{"id":"https://openalex.org/C205260736","wikidata":"https://www.wikidata.org/wiki/Q418939","display_name":"Heat shock protein","level":3,"score":0.23236781358718872},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1464838683605194},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":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":"D018840","descriptor_name":"HSP70 Heat-Shock Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018840","descriptor_name":"HSP70 Heat-Shock Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018840","descriptor_name":"HSP70 Heat-Shock Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz670","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz670","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/735/32369857/btz670.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31504177","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31504177","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz670","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz670","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/735/32369857/btz670.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.550000011920929,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1046470221","https://openalex.org/W1861846019","https://openalex.org/W1966716734","https://openalex.org/W1980459682","https://openalex.org/W1983137299","https://openalex.org/W1997718936","https://openalex.org/W2006877285","https://openalex.org/W2008972431","https://openalex.org/W2023490488","https://openalex.org/W2023612866","https://openalex.org/W2040615922","https://openalex.org/W2052257078","https://openalex.org/W2058759643","https://openalex.org/W2076945013","https://openalex.org/W2109936231","https://openalex.org/W2110574412","https://openalex.org/W2119714298","https://openalex.org/W2129194339","https://openalex.org/W2142774061","https://openalex.org/W2414920179","https://openalex.org/W2478642516","https://openalex.org/W2580712204","https://openalex.org/W2601312386","https://openalex.org/W2778339596","https://openalex.org/W2779495351","https://openalex.org/W2904223696"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W157115903","https://openalex.org/W2789551765","https://openalex.org/W2133301860","https://openalex.org/W2121503534","https://openalex.org/W1974211771"],"abstract_inverted_index":{"MOTIVATION:":[0],"Understanding":[1],"the":[2,15,19,115],"mechanisms":[3],"of":[4,21,31,39,47,80,124,155],"client":[5],"protein":[6],"interaction":[7,116],"with":[8],"Hsp70":[9,27,48,93],"chaperones":[10],"is":[11,146,157],"essential":[12],"to":[13,63,66,91,136],"analyze":[14],"complex":[16],"dynamics":[17],"in":[18,37,44,53,96,130,134,148],"context":[20],"normal":[22],"or":[23,105,127],"dysregulated":[24],"metabolism.":[25],"Because":[26],"can":[28],"bind":[29],"millions":[30],"proteins,":[32],"including":[33],"key":[34],"molecules":[35],"involved":[36],"processes":[38],"stemness,":[40],"tumorigenesis":[41],"and":[42,77,83,119],"survival,":[43],"silico":[45],"prediction":[46],"interactions":[49],"has":[50],"great":[51],"value":[52],"validating":[54],"possible":[55],"new":[56,89],"clients.":[57],"Currently,":[58],"two":[59],"algorithms":[60],"are":[61,71,168],"available":[62,159,169],"predict":[64],"binding":[65,94,140],"DnaK-the":[67],"bacterial":[68],"Hsp70-but":[69],"both":[70],"based":[72],"on":[73,102],"amino":[74],"acid":[75],"sequence":[76],"energy":[78],"calculations":[79],"qualitative":[81,104,126],"information-binders":[82],"non-binders.":[84],"RESULTS:":[85],"We":[86],"introduce":[87],"a":[88],"algorithm":[90],"identify":[92],"sequences":[95],"proteins-ChaperISM-a":[97],"position-independent":[98],"scoring":[99],"matrix":[100],"trained":[101],"either":[103],"quantitative":[106],"chemiluminescence":[107],"data":[108,167],"previously":[109],"published,":[110],"which":[111],"were":[112],"obtained":[113],"from":[114],"between":[117],"DnaK":[118],"different":[120],"ligands.":[121],"Both":[122],"versions":[123],"ChaperISM,":[125],"quantitative,":[128],"resulted":[129],"an":[131],"improved":[132],"performance":[133],"comparison":[135],"other":[137],"state-of-the-art":[138],"chaperone":[139],"predictors.":[141],"AVAILABILITY":[142],"AND":[143],"IMPLEMENTATION:":[144],"ChaperISM":[145,156],"implemented":[147],"Python":[149],"version":[150],"3.":[151],"The":[152],"source":[153],"code":[154],"freely":[158],"for":[160],"download":[161],"at":[162,170],"https://github.com/BioinfLab/ChaperISM.":[163],"SUPPLEMENTARY":[164],"INFORMATION:":[165],"Supplementary":[166],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-02T14:50:37.381335","created_date":"2025-10-10T00:00:00"}