{"id":"https://openalex.org/W3159318882","doi":"https://doi.org/10.1093/bioinformatics/btab253","title":"Protlego: a Python package for the analysis and design of chimeric proteins","display_name":"Protlego: a Python package for the analysis and design of chimeric proteins","publication_year":2021,"publication_date":"2021-04-19","ids":{"openalex":"https://openalex.org/W3159318882","doi":"https://doi.org/10.1093/bioinformatics/btab253","mag":"3159318882","pmid":"https://pubmed.ncbi.nlm.nih.gov/33901273"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab253","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab253","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3182/40556851/btab253.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3182/40556851/btab253.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004684799","display_name":"Noelia Ferruz","orcid":"https://orcid.org/0000-0003-4172-8201"},"institutions":[{"id":"https://openalex.org/I54009628","display_name":"University of Bayreuth","ror":"https://ror.org/0234wmv40","country_code":"DE","type":"education","lineage":["https://openalex.org/I54009628"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Noelia Ferruz","raw_affiliation_strings":["Department of Biochemistry, University of Bayreuth , 95447 Bayreuth, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Bayreuth , 95447 Bayreuth, Germany","institution_ids":["https://openalex.org/I54009628"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016245091","display_name":"Jakob Noske","orcid":"https://orcid.org/0000-0001-7763-2645"},"institutions":[{"id":"https://openalex.org/I54009628","display_name":"University of Bayreuth","ror":"https://ror.org/0234wmv40","country_code":"DE","type":"education","lineage":["https://openalex.org/I54009628"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jakob Noske","raw_affiliation_strings":["Department of Biochemistry, University of Bayreuth , 95447 Bayreuth, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Bayreuth , 95447 Bayreuth, Germany","institution_ids":["https://openalex.org/I54009628"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063262156","display_name":"Birte H\u00f6cker","orcid":"https://orcid.org/0000-0002-8250-9462"},"institutions":[{"id":"https://openalex.org/I54009628","display_name":"University of Bayreuth","ror":"https://ror.org/0234wmv40","country_code":"DE","type":"education","lineage":["https://openalex.org/I54009628"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Birte H\u00f6cker","raw_affiliation_strings":["Department of Biochemistry, University of Bayreuth , 95447 Bayreuth, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Bayreuth , 95447 Bayreuth, Germany","institution_ids":["https://openalex.org/I54009628"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5063262156"],"corresponding_institution_ids":["https://openalex.org/I54009628"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2213,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.78494218,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"37","issue":"19","first_page":"3182","last_page":"3189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.40790000557899475,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.40790000557899475,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.1298000067472458,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.08900000154972076,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7392235398292542},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6889916062355042},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.46530160307884216},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4262581467628479},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42056751251220703},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3831040859222412},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2829420566558838}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7392235398292542},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6889916062355042},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.46530160307884216},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4262581467628479},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42056751251220703},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3831040859222412},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2829420566558838}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab253","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab253","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3182/40556851/btab253.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33901273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33901273","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8504633","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8504633","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab253","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab253","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/19/3182/40556851/btab253.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2625829991","display_name":"Protein design from sub-domain sized fragments","funder_award_id":"647548","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"},{"id":"https://openalex.org/G7450196404","display_name":null,"funder_award_id":"94747","funder_id":"https://openalex.org/F4320320882","funder_display_name":"Volkswagen Foundation"}],"funders":[{"id":"https://openalex.org/F4320320882","display_name":"Volkswagen Foundation","ror":"https://ror.org/03bsmfz84"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W124504601","https://openalex.org/W1834588461","https://openalex.org/W1965827393","https://openalex.org/W1969644422","https://openalex.org/W1976442731","https://openalex.org/W1976603396","https://openalex.org/W1984512623","https://openalex.org/W1985603295","https://openalex.org/W1991456646","https://openalex.org/W1999104032","https://openalex.org/W2003675367","https://openalex.org/W2004510362","https://openalex.org/W2006831136","https://openalex.org/W2007595404","https://openalex.org/W2013404472","https://openalex.org/W2023790301","https://openalex.org/W2029667189","https://openalex.org/W2031903428","https://openalex.org/W2038089463","https://openalex.org/W2067944903","https://openalex.org/W2070753604","https://openalex.org/W2071161999","https://openalex.org/W2074069606","https://openalex.org/W2076542022","https://openalex.org/W2083565918","https://openalex.org/W2089597488","https://openalex.org/W2099560117","https://openalex.org/W2102245393","https://openalex.org/W2111686080","https://openalex.org/W2115540209","https://openalex.org/W2123503816","https://openalex.org/W2130479394","https://openalex.org/W2131128775","https://openalex.org/W2136593531","https://openalex.org/W2141346454","https://openalex.org/W2145268834","https://openalex.org/W2147988069","https://openalex.org/W2151550848","https://openalex.org/W2159010139","https://openalex.org/W2161072217","https://openalex.org/W2172281886","https://openalex.org/W2173280871","https://openalex.org/W2201713963","https://openalex.org/W2211953232","https://openalex.org/W2282054059","https://openalex.org/W2292512133","https://openalex.org/W2296686360","https://openalex.org/W2345741266","https://openalex.org/W2419588362","https://openalex.org/W2421664314","https://openalex.org/W2523172184","https://openalex.org/W2525712686","https://openalex.org/W2558272290","https://openalex.org/W2893131760","https://openalex.org/W2902051551","https://openalex.org/W2949223833","https://openalex.org/W2971733377","https://openalex.org/W2999044305","https://openalex.org/W3012951261","https://openalex.org/W3018526736","https://openalex.org/W3113219874","https://openalex.org/W4234287785","https://openalex.org/W6649554704"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W2618286804","https://openalex.org/W3116064965","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"MOTIVATION:":[0],"Duplication":[1],"and":[2,36,71,79,99,121,163,168,171,193,197,225,233],"recombination":[3,31],"of":[4,26,45,52,69,82,90,119],"protein":[5,13,27,213],"fragments":[6,130],"have":[7],"led":[8],"to":[9],"the":[10,24,43,83,88,166,188,191,212,222],"highly":[11],"diverse":[12,173],"space":[14],"that":[15,64,114,204],"we":[16,182],"observe":[17],"today.":[18],"By":[19],"mimicking":[20],"this":[21],"natural":[22,158],"process,":[23],"design":[25,44,118,214],"chimeras":[28,120,156],"via":[29,145,153],"fragment":[30],"has":[32,37],"proven":[33],"experimentally":[34],"successful":[35],"opened":[38],"a":[39,61,66,111,132,207],"new":[40,209],"era":[41],"for":[42,55,75,150,211],"customizable":[46],"proteins.":[47],"The":[48],"in":[49,101],"silico":[50],"building":[51,196],"structural":[53,80,123,174],"models":[54],"these":[56],"chimeric":[57],"proteins,":[58],"however,":[59],"remains":[60],"manual":[62],"task":[63],"requires":[65],"considerable":[67],"degree":[68],"expertise":[70],"is":[72,226],"not":[73],"amenable":[74],"high-throughput":[76,117],"studies.":[77],"Energetic":[78],"analysis":[81],"designed":[84],"proteins":[85,159],"often":[86],"require":[87],"use":[89],"several":[91],"tools,":[92],"each":[93],"with":[94,165,231],"their":[95,122,172,199],"unique":[96],"technical":[97],"difficulties":[98],"available":[100,136,228,240],"different":[102],"programming":[103],"languages":[104],"or":[105,147,157],"web":[106],"servers.":[107],"RESULTS:":[108],"We":[109,202],"implemented":[110],"Python":[112],"package":[113],"enables":[115],"automated,":[116],"analysis.":[124],"First,":[125],"it":[126],"fetches":[127],"evolutionarily":[128],"conserved":[129],"from":[131],"built-in":[133],"database":[134],"(also":[135],"at":[137,179,229,241],"fuzzle.uni-bayreuth.de).":[138],"These":[139],"relationships":[140,189],"can":[141,176],"then":[142,161],"be":[143,177],"represented":[144],"networks":[146],"further":[148],"selected":[149],"chimera":[151],"construction":[152],"recombination.":[154],"Designed":[155],"are":[160,239],"scored":[162],"minimized":[164],"Charmm":[167],"Amber":[169],"forcefields":[170],"features":[175],"analyzed":[178],"ease.":[180],"Here,":[181],"showcase":[183],"Protlego's":[184],"pipeline":[185],"by":[186],"exploring":[187],"between":[190],"P-loop":[192],"Rossmann":[194],"superfolds,":[195],"characterizing":[198],"offspring":[200],"chimeras.":[201],"believe":[203],"Protlego":[205,219],"provides":[206],"powerful":[208],"tool":[210],"community.":[215],"AVAILABILITY":[216],"AND":[217],"IMPLEMENTATION:":[218],"runs":[220],"on":[221],"Linux":[223],"platform":[224],"freely":[227],"(https://hoecker-lab.github.io/protlego/)":[230],"tutorials":[232],"documentation.":[234],"SUPPLEMENTARY":[235],"INFORMATION:":[236],"Supplementary":[237],"data":[238],"Bioinformatics":[242],"online.":[243]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4}],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2025-10-10T00:00:00"}
