{"id":"https://openalex.org/W2170203299","doi":"https://doi.org/10.1093/bioinformatics/btt402","title":"pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling","display_name":"pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling","publication_year":2013,"publication_date":"2013-07-10","ids":{"openalex":"https://openalex.org/W2170203299","doi":"https://doi.org/10.1093/bioinformatics/btt402","mag":"2170203299","pmid":"https://pubmed.ncbi.nlm.nih.gov/23846743"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt402","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2363/50782218/bioinformatics_29_18_2363.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":"software-paper","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2363/50782218/bioinformatics_29_18_2363.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114031262","display_name":"V. Gil","orcid":null},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"V\u00edctor A. Gil","raw_affiliation_strings":["1 Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, E-08010 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, E-08010 Barcelona, Spain","institution_ids":["https://openalex.org/I11932220","https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060698638","display_name":"V\u0131\u0301ctor Guallar","orcid":"https://orcid.org/0000-0002-4580-1114"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"V\u00edctor Guallar","raw_affiliation_strings":["1 Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, E-08010 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Llu\u00eds Companys 23, E-08010 Barcelona, Spain","institution_ids":["https://openalex.org/I11932220","https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060698638"],"corresponding_institution_ids":["https://openalex.org/I11932220","https://openalex.org/I2799803557","https://openalex.org/I9617848"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"29","issue":"18","first_page":"2363","last_page":"2364"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.2639999985694885,"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":0.2639999985694885,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.19120000302791595,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.10779999941587448,"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":0.9007661938667297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7907803058624268},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6891971230506897},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5694778561592102},{"id":"https://openalex.org/keywords/workbench","display_name":"Workbench","score":0.5664291381835938},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4995918273925781},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.47843530774116516},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4611611068248749},{"id":"https://openalex.org/keywords/extensibility","display_name":"Extensibility","score":0.44705501198768616},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4444355070590973},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43777936697006226},{"id":"https://openalex.org/keywords/unit-testing","display_name":"Unit testing","score":0.41000494360923767},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35179829597473145},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2825854420661926},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15946844220161438},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.15138885378837585}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9007661938667297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7907803058624268},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6891971230506897},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5694778561592102},{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.5664291381835938},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4995918273925781},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.47843530774116516},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4611611068248749},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.44705501198768616},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4444355070590973},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43777936697006226},{"id":"https://openalex.org/C148027188","wikidata":"https://www.wikidata.org/wiki/Q907375","display_name":"Unit testing","level":3,"score":0.41000494360923767},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35179829597473145},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2825854420661926},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15946844220161438},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.15138885378837585}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt402","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2363/50782218/bioinformatics_29_18_2363.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:23846743","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23846743","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/btt402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt402","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/18/2363/50782218/bioinformatics_29_18_2363.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/9","score":0.44999998807907104,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170203299.pdf","grobid_xml":"https://content.openalex.org/works/W2170203299.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1991745348","https://openalex.org/W2025296083","https://openalex.org/W2108107014","https://openalex.org/W2122576346","https://openalex.org/W2132914434"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W1590168840","https://openalex.org/W2113128227","https://openalex.org/W2061990085","https://openalex.org/W4225687299","https://openalex.org/W2113066987","https://openalex.org/W3081674575","https://openalex.org/W4287673983","https://openalex.org/W2885293781","https://openalex.org/W3123068371"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"introduce":[2],"pyRMSD,":[3],"an":[4,14],"open":[5],"source":[6,126],"standalone":[7],"Python":[8,94],"package":[9],"that":[10,65],"aims":[11],"at":[12,139,153],"offering":[13],"integrative":[15],"and":[16,78,104,134],"efficient":[17],"way":[18],"of":[19,27,30,92,115],"performing":[20],"Root":[21],"Mean":[22],"Square":[23],"Deviation":[24],"(RMSD)-related":[25],"calculations":[26],"large":[28],"sets":[29],"structures.":[31],"It":[32],"is":[33],"specially":[34],"tuned":[35],"to":[36,48,75,111],"do":[37],"fast":[38],"collective":[39],"RMSD":[40,44],"calculations,":[41],"as":[42,70],"pairwise":[43],"matrices,":[45],"implementing":[46],"up":[47],"three":[49],"well-known":[50],"superposition":[51],"algorithms.":[52,123],"pyRMSD":[53],"provides":[54],"its":[55,100],"own":[56],"symmetric":[57],"distance":[58],"matrix":[59],"class":[60],"that,":[61],"besides":[62],"the":[63,89,142],"fact":[64],"it":[66,107],"can":[67,86,136],"be":[68,137],"used":[69],"a":[71,108,116],"regular":[72],"matrix,":[73],"helps":[74],"save":[76],"memory":[77,80],"increases":[79],"access":[81],"speed.":[82],"This":[83],"last":[84],"feature":[85],"dramatically":[87],"improve":[88],"overall":[90],"performance":[91],"any":[93],"algorithm":[95],"using":[96],"it.":[97],"In":[98],"addition,":[99],"extensibility,":[101],"testing":[102,121],"suites":[103,133],"documentation":[105],"make":[106],"good":[109],"choice":[110],"those":[112],"in":[113],"need":[114],"workbench":[117],"for":[118],"developing":[119],"or":[120],"new":[122],"AVAILABILITY:":[124],"The":[125],"code":[127],"(under":[128],"MIT":[129],"license),":[130],"installer,":[131],"test":[132],"benchmarks":[135],"found":[138],"https://pele.bsc.es/":[140],"under":[141],"tools":[143],"section.":[144],"CONTACT:":[145],"victor.guallar@bsc.es":[146],"SUPPLEMENTARY":[147],"INFORMATION:":[148],"Supplementary":[149],"data":[150],"are":[151],"available":[152],"Bioinformatics":[154],"online.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
