{"id":"https://openalex.org/W4409640798","doi":"https://doi.org/10.1371/journal.pcbi.1012837","title":"mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data","display_name":"mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data","publication_year":2025,"publication_date":"2025-04-21","ids":{"openalex":"https://openalex.org/W4409640798","doi":"https://doi.org/10.1371/journal.pcbi.1012837","pmid":"https://pubmed.ncbi.nlm.nih.gov/40258031"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012837","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012837","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012837","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000128747","display_name":"Guillermo P\u00e9rez\u2010Hern\u00e1ndez","orcid":"https://orcid.org/0000-0002-9287-8704"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Guillermo P\u00e9rez-Hern\u00e1ndez","raw_affiliation_strings":["Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9287-8704","affiliations":[{"raw_affiliation_string":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I7877124","https://openalex.org/I75951250"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070831090","display_name":"Peter W. Hildebrand","orcid":"https://orcid.org/0000-0003-0063-1104"},"institutions":[{"id":"https://openalex.org/I33256026","display_name":"German Research Centre for Artificial Intelligence","ror":"https://ror.org/01ayc5b57","country_code":"DE","type":"funder","lineage":["https://openalex.org/I33256026"]},{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I4401726909","display_name":"Center for Scalable Data Analytics and Artificial Intelligence","ror":"https://ror.org/01t4ttr56","country_code":"DE","type":"education","lineage":["https://openalex.org/I4401726909","https://openalex.org/I78650965","https://openalex.org/I926574661"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter W. Hildebrand","raw_affiliation_strings":["Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin, Berlin, Germany","Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany","Universit\u00e4t Leipzig, Medizinische Fakult\u00e4t, Institut f\u00fcr Medizinische Physik und Biophysik, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany","institution_ids":["https://openalex.org/I33256026","https://openalex.org/I4401726909"]},{"raw_affiliation_string":"Universit\u00e4t Leipzig, Medizinische Fakult\u00e4t, Institut f\u00fcr Medizinische Physik und Biophysik, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.7596,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.96409563,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"4","first_page":"e1012837","last_page":"e1012837"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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":0.8066679239273071},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8026492595672607},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6325042843818665},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5694474577903748},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.5671498775482178},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5431108474731445},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.529930055141449},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.523657500743866},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.45346251130104065},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.44976478815078735},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.43353572487831116},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4220826029777527},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4177358150482178},{"id":"https://openalex.org/keywords/numbering","display_name":"Numbering","score":0.41699787974357605},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.4131011664867401},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.37161242961883545},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35329461097717285},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26893413066864014},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.17607295513153076},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1565246880054474}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8066679239273071},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8026492595672607},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6325042843818665},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5694474577903748},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.5671498775482178},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5431108474731445},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.529930055141449},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.523657500743866},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45346251130104065},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.44976478815078735},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.43353572487831116},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4220826029777527},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4177358150482178},{"id":"https://openalex.org/C191916993","wikidata":"https://www.wikidata.org/wiki/Q362019","display_name":"Numbering","level":2,"score":0.41699787974357605},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.4131011664867401},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37161242961883545},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35329461097717285},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26893413066864014},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.17607295513153076},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1565246880054474},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012837","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012837","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40258031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40258031","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:8a8ab980517947e785ebe504a2705392","is_oa":true,"landing_page_url":"https://doaj.org/article/8a8ab980517947e785ebe504a2705392","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 4, p e1012837 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12011235","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12011235","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012837","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012837","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7225806244","display_name":null,"funder_award_id":"SFB1423, project 421152132, subproject C01 and Z04","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320328160","display_name":"Stiftung Charit\u00e9","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1199870172","https://openalex.org/W1833104430","https://openalex.org/W1966078827","https://openalex.org/W1975436091","https://openalex.org/W2029667189","https://openalex.org/W2049902088","https://openalex.org/W2075243501","https://openalex.org/W2114850508","https://openalex.org/W2132629607","https://openalex.org/W2147988069","https://openalex.org/W2170711116","https://openalex.org/W2225513621","https://openalex.org/W2226825552","https://openalex.org/W2332712348","https://openalex.org/W2557873992","https://openalex.org/W2772099288","https://openalex.org/W2772618362","https://openalex.org/W2892113269","https://openalex.org/W2898671507","https://openalex.org/W2991285488","https://openalex.org/W3003257820","https://openalex.org/W3042198040","https://openalex.org/W3093634533","https://openalex.org/W3106745904","https://openalex.org/W3110608978","https://openalex.org/W3112376646","https://openalex.org/W3127277789","https://openalex.org/W3159156584","https://openalex.org/W3159177617","https://openalex.org/W3159719254","https://openalex.org/W3177828909","https://openalex.org/W3203735717","https://openalex.org/W4367673903","https://openalex.org/W4386583624","https://openalex.org/W4386897003","https://openalex.org/W4388464011","https://openalex.org/W4391673325","https://openalex.org/W4399561252","https://openalex.org/W4399586164","https://openalex.org/W4399817933"],"related_works":["https://openalex.org/W2380905223","https://openalex.org/W2316187651","https://openalex.org/W2005053760","https://openalex.org/W74604206","https://openalex.org/W1485272726","https://openalex.org/W2339556925","https://openalex.org/W4319083705","https://openalex.org/W2372287279","https://openalex.org/W2364846444","https://openalex.org/W1955431138"],"abstract_inverted_index":{"We":[0],"present":[1],"mdciao,":[2],"an":[3],"open-source":[4],"command":[5],"line":[6],"tool":[7],"and":[8,16,41,74,80,91,104,137,141,160,164,169],"Python":[9,121],"Application-Programming-Interface":[10],"(API)":[11],"for":[12,55,61,87,101],"easy,":[13],"one-shot":[14],"analysis":[15,40,135],"representation":[17],"of":[18,30,38,82,110],"molecular":[19],"dynamics":[20],"(MD)":[21],"simulation":[22],"data.":[23],"Building":[24],"upon":[25],"the":[26,118,127,151,165],"widely":[27],"used":[28],"concept":[29],"residue-residue":[31],"contact-frequencies,":[32],"mdciao":[33,131],"offers":[34,52],"a":[35],"wide":[36],"spectrum":[37],"further":[39],"representations,":[42],"enriched":[43],"with":[44],"available":[45],"domain":[46],"specific":[47],"annotations.":[48],"The":[49,145],"user-friendly":[50],"interface":[51],"pre-packaged":[53],"solutions":[54],"non-expert":[56],"users,":[57],"while":[58],"keeping":[59],"customizability":[60],"expert":[62],"ones.":[63],"Emphasis":[64],"has":[65],"been":[66],"put":[67],"into":[68],"automatically":[69],"producing":[70],"annotated,":[71],"production-ready":[72],"figures":[73],"tables.":[75],"Furthermore,":[76],"seamless":[77],"on-the-fly":[78],"query":[79],"inclusion":[81],"domain-specific":[83],"generic":[84],"residue":[85],"numbering":[86],"GPCRs,":[88],"GAIN-domains,":[89],"G-proteins,":[90],"kinases":[92],"is":[93,148],"made":[94],"possible":[95],"through":[96],"online":[97],"lookups.":[98],"This":[99],"allows":[100,123],"easy":[102],"selection":[103],"comparison":[105],"across":[106],"different":[107],"systems,":[108],"regardless":[109],"sequence":[111],"identity,":[112],"target":[113],"residues":[114],"or":[115,129,158],"domains.":[116],"Finally,":[117],"fully":[119],"documented":[120],"API":[122],"users":[124],"to":[125],"include":[126],"basic":[128],"advanced":[130],"functions":[132],"in":[133],"their":[134],"workflows,":[136],"provides":[138],"numerous":[139],"examples":[140],"Jupyter":[142],"Notebook":[143],"Tutorials.":[144],"source":[146],"code":[147],"published":[149],"under":[150],"GNU":[152],"Lesser":[153],"General":[154],"Public":[155],"License":[156],"v3.0":[157],"later":[159],"hosted":[161],"on":[162],"https://github.com/gph82/mdciao,":[163],"documentation,":[166],"including":[167],"guides":[168],"examples,":[170],"can":[171],"be":[172],"found":[173],"at":[174],"https://www.mdciao.org.":[175]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
