{"id":"https://openalex.org/W4400877262","doi":"https://doi.org/10.1093/bioinformatics/btae468","title":"Melodia: a Python library for protein structure analysis","display_name":"Melodia: a Python library for protein structure analysis","publication_year":2024,"publication_date":"2024-07-01","ids":{"openalex":"https://openalex.org/W4400877262","doi":"https://doi.org/10.1093/bioinformatics/btae468","pmid":"https://pubmed.ncbi.nlm.nih.gov/39037932"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae468","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae468/58704525/btae468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae468/58704525/btae468.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043078818","display_name":"Rinaldo W. Montalv\u00e3o","orcid":"https://orcid.org/0000-0003-0929-1863"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Rinaldo W Montalv\u00e3o","raw_affiliation_strings":["Rega Insitute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences , Herestraat 49 , Leuven 3000, Belgium"],"raw_orcid":"https://orcid.org/0000-0003-0929-1863","affiliations":[{"raw_affiliation_string":"Rega Insitute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences , Herestraat 49 , Leuven 3000, Belgium","institution_ids":["https://openalex.org/I24156275"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083404013","display_name":"William R. Pitt","orcid":"https://orcid.org/0000-0001-8164-4550"},"institutions":[{"id":"https://openalex.org/I4210148098","display_name":"Evotec (United Kingdom)","ror":"https://ror.org/04qvy9k41","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210130816","https://openalex.org/I4210148098"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"William R Pitt","raw_affiliation_strings":["Evotec (UK) , 95 Park Drive, Milton Park , Abingdon, Oxfordshire OX14 4RY, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-8164-4550","affiliations":[{"raw_affiliation_string":"Evotec (UK) , 95 Park Drive, Milton Park , Abingdon, Oxfordshire OX14 4RY, United Kingdom","institution_ids":["https://openalex.org/I4210148098"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064588864","display_name":"Vitor B. Pinheiro","orcid":"https://orcid.org/0000-0003-2491-0028"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Vitor B Pinheiro","raw_affiliation_strings":["Rega Insitute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences , Herestraat 49 , Leuven 3000, Belgium"],"raw_orcid":"https://orcid.org/0000-0003-2491-0028","affiliations":[{"raw_affiliation_string":"Rega Insitute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences , Herestraat 49 , Leuven 3000, Belgium","institution_ids":["https://openalex.org/I24156275"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001029093","display_name":"Tom L. Blundell","orcid":"https://orcid.org/0000-0002-2708-8992"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tom L Blundell","raw_affiliation_strings":["Heart and Lung Research Institute, University of Cambridge, Biomedical Campus , Trumpington, Cambridgeshire CB2 0BB, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-2708-8992","affiliations":[{"raw_affiliation_string":"Heart and Lung Research Institute, University of Cambridge, Biomedical Campus , Trumpington, Cambridgeshire CB2 0BB, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5043078818"],"corresponding_institution_ids":["https://openalex.org/I24156275"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1056,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.37198193,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"40","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.5329999923706055,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.5329999923706055,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.1298999935388565,"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":0.09390000253915787,"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/python","display_name":"Python (programming language)","score":0.9504162073135376},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5962876081466675},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5010504722595215},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38751107454299927},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21235373616218567}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9504162073135376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5962876081466675},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5010504722595215},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38751107454299927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21235373616218567}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btae468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae468","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae468/58704525/btae468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:39037932","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39037932","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:lirias2repo.kuleuven.be:20.500.12942/745848","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/20.500.12942/745848","pdf_url":"https://lirias.kuleuven.be/bitstream/20.500.12942/745848/3/btae468.pdf","source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"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, vol. 40 (7), Art.No. btae468","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:11290362","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11290362","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11290362/pdf/btae468.pdf","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"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/372042","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/372042","pdf_url":"https://www.repository.cam.ac.uk/bitstreams/e0efaac3-1869-404a-92a1-05a10e3298e8/download","source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":null,"raw_type":"Other"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae468","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae468/58704525/btae468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G5400932032","display_name":null,"funder_award_id":"C14/19/102","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5653589078","display_name":null,"funder_award_id":"C14/19","funder_id":"https://openalex.org/F4320322308","funder_display_name":"KU Leuven"},{"id":"https://openalex.org/G5987555810","display_name":null,"funder_award_id":"C14/19/102","funder_id":"https://openalex.org/F4320322308","funder_display_name":"KU Leuven"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320322308","display_name":"KU Leuven","ror":"https://ror.org/05f950310"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null},{"id":"https://openalex.org/F4320330538","display_name":"Rega Foundation","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400877262.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W95014119","https://openalex.org/W101364403","https://openalex.org/W1864728009","https://openalex.org/W1998586260","https://openalex.org/W2000578081","https://openalex.org/W2004156590","https://openalex.org/W2022012484","https://openalex.org/W2039824457","https://openalex.org/W2053289437","https://openalex.org/W2062611338","https://openalex.org/W2075682762","https://openalex.org/W2077605547","https://openalex.org/W2078121608","https://openalex.org/W2098322708","https://openalex.org/W2101234009","https://openalex.org/W2114850508","https://openalex.org/W2151785844","https://openalex.org/W2186440999","https://openalex.org/W2477171630","https://openalex.org/W2736977076","https://openalex.org/W2772099288","https://openalex.org/W2906517282","https://openalex.org/W2971108811","https://openalex.org/W3003257820","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3103145119","https://openalex.org/W3129020707","https://openalex.org/W4200499082","https://openalex.org/W4245532735","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"SUMMARY:":[0],"Analysing":[1],"protein":[2,10,75],"structure":[3],"similarities":[4],"is":[5,56,126],"an":[6,41,127],"important":[7],"step":[8],"in":[9,40,96],"engineering":[11],"and":[12,36,47,70,83,119],"drug":[13],"discovery.":[14],"Methodologies":[15],"that":[16],"are":[17,23,103,145],"more":[18,52,104],"advanced":[19,53],"than":[20,110],"simple":[21],"RMSD":[22,111],"available":[24,132,146],"but":[25],"often":[26],"require":[27],"extensive":[28],"mathematical":[29],"or":[30],"computational":[31],"knowledge":[32],"for":[33,67,92],"implementation.":[34],"Grouping":[35],"optimising":[37],"such":[38],"tools":[39],"efficient":[42],"open-source":[43,128],"library":[44,59,130],"increases":[45],"accessibility":[46],"encourages":[48],"the":[49,72],"adoption":[50],"of":[51,64,74,80,94],"metrics.":[54],"Melodia":[55,113,125],"a":[57,61,98],"Python":[58,129],"with":[60,136],"complete":[62],"set":[63],"components":[65],"devised":[66],"describing,":[68],"comparing":[69],"analysing":[71],"shape":[73],"structures":[76],"using":[77],"differential":[78],"geometry":[79],"three-dimensional":[81,120],"curves":[82],"knot":[84],"theory.":[85],"It":[86],"can":[87],"generate":[88],"robust":[89],"geometric":[90],"descriptors":[91,102],"thousands":[93],"shapes":[95],"just":[97],"few":[99],"minutes.":[100],"Those":[101],"sensitive":[105],"to":[106],"structural":[107,117],"feature":[108],"variation":[109],"deviation.":[112],"also":[114],"incorporates":[115],"sequence":[116],"annotation":[118],"visualisations.":[121],"AVAILABILITY":[122],"AND":[123],"IMPLEMENTATION:":[124],"freely":[131],"on":[133],"https://github.com/rwmontalvao/Melodia_py,":[134],"along":[135],"interactive":[137],"Jupyter":[138],"Notebook":[139],"tutorials.":[140],"SUPPLEMENTARY":[141],"INFORMATION:":[142],"Supplementary":[143],"data":[144],"at":[147],"Bioinformatics":[148],"online.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
