{"id":"https://openalex.org/W2323614149","doi":"https://doi.org/10.1093/bioinformatics/btw129","title":"mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories","display_name":"mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories","publication_year":2016,"publication_date":"2016-04-07","ids":{"openalex":"https://openalex.org/W2323614149","doi":"https://doi.org/10.1093/bioinformatics/btw129","mag":"2323614149","pmid":"https://pubmed.ncbi.nlm.nih.gov/27153575"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw129","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2531/49020649/bioinformatics_32_16_2531.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/32/16/2531/49020649/bioinformatics_32_16_2531.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042029425","display_name":"Kota Kasahara","orcid":"https://orcid.org/0000-0003-0207-6271"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kota Kasahara","raw_affiliation_strings":["Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014939908","display_name":"Neetha Mohan","orcid":"https://orcid.org/0000-0001-5204-6463"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Neetha Mohan","raw_affiliation_strings":["Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063926612","display_name":"Ikuo Fukuda","orcid":"https://orcid.org/0000-0001-8668-7197"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ikuo Fukuda","raw_affiliation_strings":["Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035143113","display_name":"Haruki Nakamura","orcid":"https://orcid.org/0000-0001-6690-5863"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Haruki Nakamura","raw_affiliation_strings":["Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5042029425"],"corresponding_institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3417,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.67298239,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"32","issue":"16","first_page":"2531","last_page":"2533"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7336999773979187,"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":0.7336999773979187,"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/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.020500000566244125,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.013100000098347664,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.7029191255569458},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5964317321777344},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5809720754623413},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5600942969322205},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3848220705986023},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3731590509414673},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3714398443698883},{"id":"https://openalex.org/keywords/classical-mechanics","display_name":"Classical mechanics","score":0.3541821837425232},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20996534824371338},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19548875093460083},{"id":"https://openalex.org/keywords/acoustics","display_name":"Acoustics","score":0.18962761759757996},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.10216358304023743}],"concepts":[{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.7029191255569458},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5964317321777344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5809720754623413},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5600942969322205},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3848220705986023},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3731590509414673},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3714398443698883},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.3541821837425232},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20996534824371338},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19548875093460083},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.18962761759757996},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.10216358304023743},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","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":"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:10.1093/bioinformatics/btw129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw129","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2531/49020649/bioinformatics_32_16_2531.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27153575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27153575","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:europepmc.org:3943374","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4978922","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/16/2531","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/16/2531","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw129","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw129","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2531/49020649/bioinformatics_32_16_2531.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3291055677","display_name":null,"funder_award_id":"24118008","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320314183","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338065","display_name":"Institute of Genetics","ror":"https://ror.org/03gwhmn95"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2323614149.pdf","grobid_xml":"https://content.openalex.org/works/W2323614149.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1986719264","https://openalex.org/W1995775850","https://openalex.org/W2029667189","https://openalex.org/W2076949721","https://openalex.org/W2159675211","https://openalex.org/W2160544821","https://openalex.org/W2170711116","https://openalex.org/W3088604011"],"related_works":["https://openalex.org/W2023156907","https://openalex.org/W2379392295","https://openalex.org/W3160965418","https://openalex.org/W1968806281","https://openalex.org/W3095515585","https://openalex.org/W613940353","https://openalex.org/W4315498887","https://openalex.org/W2320915480","https://openalex.org/W4238727794","https://openalex.org/W1481030933"],"abstract_inverted_index":{"UNLABELLED:":[0],"We":[1,64],"previously":[2],"reported":[3],"the":[4,19,53,81,85],"multi-modal":[5,27],"Dynamic":[6],"Cross":[7],"Correlation":[8],"(mDCC)":[9],"method":[10,17],"for":[11,51,77,103],"analyzing":[12],"molecular":[13],"dynamics":[14],"trajectories.":[15],"This":[16],"quantifies":[18],"correlation":[20],"coefficients":[21],"of":[22,84,89],"atomic":[23],"motions":[24],"with":[25],"complex":[26,59],"behaviors":[28],"by":[29],"using":[30,80],"a":[31,66],"Bayesian-based":[32],"pattern":[33,57],"recognition":[34],"technique":[35],"that":[36,69],"can":[37],"effectively":[38],"capture":[39],"transiently":[40],"formed,":[41],"unstable":[42],"interactions.":[43],"Here,":[44],"we":[45],"present":[46],"an":[47,78,90],"open":[48],"source":[49,99],"toolkit":[50,76],"performing":[52],"mDCC":[54],"analysis,":[55,79],"including":[56],"recognitions,":[58],"network":[60],"analyses":[61],"and":[62,111,113],"visualizations.":[63],"include":[65],"tutorial":[67],"document":[68],"thoroughly":[70],"explains":[71],"how":[72],"to":[73],"apply":[74],"this":[75],"example":[82],"trajectory":[83],"100":[86],"ns":[87],"simulation":[88],"engineered":[91],"endothelin-1":[92],"peptide":[93],"dimer.":[94],"AVAILABILITY":[95],"AND":[96],"IMPLEMENTATION:":[97],"The":[98],"code":[100],"is":[101],"available":[102,124],"free":[104],"at":[105,125],"http://www.protein.osaka-u.ac.jp/rcsfp/pi/mdcctools/,":[106],"implemented":[107],"in":[108],"C":[109],"++":[110],"Python,":[112],"supported":[114],"on":[115],"Linux.":[116],"CONTACT:":[117],"kota.kasahara@protein.osaka-u.ac.jp":[118],"SUPPLEMENTARY":[119],"INFORMATION:":[120],"Supplementary":[121],"data":[122],"are":[123],"Bioinformatics":[126],"online.":[127]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
