{"id":"https://openalex.org/W4387636992","doi":"https://doi.org/10.1093/bib/bbad357","title":"Searching similar local 3D micro-environments in protein structure databases with MicroMiner","display_name":"Searching similar local 3D micro-environments in protein structure databases with MicroMiner","publication_year":2023,"publication_date":"2023-09-22","ids":{"openalex":"https://openalex.org/W4387636992","doi":"https://doi.org/10.1093/bib/bbad357","pmid":"https://pubmed.ncbi.nlm.nih.gov/37833838"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad357","pdf_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad357/52631904/bbad357.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad357/52631904/bbad357.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055412887","display_name":"Jochen Sieg","orcid":"https://orcid.org/0000-0001-5343-7255"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jochen Sieg","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics , Bundesstra\u00dfe 43, 20146 Hamburg , Germany"],"affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics , Bundesstra\u00dfe 43, 20146 Hamburg , Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics , Bundesstra\u00dfe 43, 20146 Hamburg , Germany"],"affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics , Bundesstra\u00dfe 43, 20146 Hamburg , Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083205378"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.3703,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.81436903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"6","first_page":null,"last_page":null},"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/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"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9980999827384949,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.6811317801475525},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.637245774269104},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.592700183391571},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5736618041992188},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5188813805580139},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.4870813190937042},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.47943443059921265},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4735269546508789},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.45644599199295044},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4078916311264038},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4058283567428589},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.38805079460144043},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27810531854629517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25053083896636963},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.23566606640815735},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.19635039567947388},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08642798662185669}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.6811317801475525},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.637245774269104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.592700183391571},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5736618041992188},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5188813805580139},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.4870813190937042},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.47943443059921265},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4735269546508789},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.45644599199295044},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4078916311264038},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4058283567428589},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.38805079460144043},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27810531854629517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25053083896636963},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.23566606640815735},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.19635039567947388},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08642798662185669},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad357","pdf_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad357/52631904/bbad357.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37833838","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37833838","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad357","pdf_url":"https://academic.oup.com/bib/article-pdf/24/6/bbad357/52631904/bbad357.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4723228088","display_name":null,"funder_award_id":"031L0105","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G5088104505","display_name":null,"funder_award_id":"de.NBI","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5965902060","display_name":null,"funder_award_id":"031B0405B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7225624288","display_name":null,"funder_award_id":"This work was","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8942490779","display_name":null,"funder_award_id":"031L0105","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387636992.pdf"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W1985600711","https://openalex.org/W1995541084","https://openalex.org/W2000061529","https://openalex.org/W2010099233","https://openalex.org/W2015292449","https://openalex.org/W2022058405","https://openalex.org/W2043481183","https://openalex.org/W2055043387","https://openalex.org/W2072052957","https://openalex.org/W2086719212","https://openalex.org/W2099672241","https://openalex.org/W2100383158","https://openalex.org/W2102245393","https://openalex.org/W2103459989","https://openalex.org/W2110947069","https://openalex.org/W2125359610","https://openalex.org/W2171962405","https://openalex.org/W2172034373","https://openalex.org/W2175728132","https://openalex.org/W2238707319","https://openalex.org/W2322633051","https://openalex.org/W2395439412","https://openalex.org/W2478474335","https://openalex.org/W2625768267","https://openalex.org/W2791661810","https://openalex.org/W2794503008","https://openalex.org/W2795970199","https://openalex.org/W2799513065","https://openalex.org/W2802078483","https://openalex.org/W2891927397","https://openalex.org/W2898210859","https://openalex.org/W2945486505","https://openalex.org/W2950954328","https://openalex.org/W2953103783","https://openalex.org/W2955704392","https://openalex.org/W2972411752","https://openalex.org/W3004119070","https://openalex.org/W3025314715","https://openalex.org/W3048947632","https://openalex.org/W3093556707","https://openalex.org/W3093646295","https://openalex.org/W3094051077","https://openalex.org/W3094967361","https://openalex.org/W3104081477","https://openalex.org/W3105751341","https://openalex.org/W3110608978","https://openalex.org/W3143063265","https://openalex.org/W3159719254","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3211795435","https://openalex.org/W4206002704","https://openalex.org/W4206940890","https://openalex.org/W4210861939","https://openalex.org/W4220705085","https://openalex.org/W4286488966","https://openalex.org/W4304084233","https://openalex.org/W4309506674","https://openalex.org/W4327566741","https://openalex.org/W4367669413","https://openalex.org/W6649447719","https://openalex.org/W6688322523","https://openalex.org/W6781185695"],"related_works":["https://openalex.org/W4388749535","https://openalex.org/W1979707045","https://openalex.org/W4285340733","https://openalex.org/W2419335570","https://openalex.org/W2584773272","https://openalex.org/W2121688928","https://openalex.org/W2084743099","https://openalex.org/W4235583582","https://openalex.org/W2106883599","https://openalex.org/W4232453105"],"abstract_inverted_index":{"The":[0],"available":[1,178],"protein":[2,45,103],"structure":[3,19,46,144],"data":[4,129],"are":[5,88],"rapidly":[6],"increasing.":[7],"Within":[8],"these":[9,26],"structures,":[10],"numerous":[11],"local":[12,42,50,111],"structural":[13,75,112,154],"sites":[14,27,43],"depict":[15],"the":[16,55,65,72,83,86,106,142,148,153,166,187],"details":[17],"characterizing":[18],"and":[20,24,29,63,85,117,171,184],"function.":[21],"However,":[22],"searching":[23],"analyzing":[25],"extensively":[28],"at":[30],"scale":[31],"poses":[32],"a":[33,37,58,180],"challenge.":[34],"We":[35,53,125],"present":[36],"new":[38,59],"method":[39,56],"to":[40,146],"search":[41,70],"in":[44,57,102],"databases":[47],"using":[48],"residue-defined":[49],"3D":[51],"micro-environments.":[52],"implemented":[54],"tool":[60,183],"called":[61],"MicroMiner":[62,163,176],"demonstrate":[64],"capabilities":[66],"of":[67,74,131],"residue":[68],"micro-environment":[69],"on":[71,186],"example":[73],"mutation":[76,134,149,169],"analysis.":[77],"Usually,":[78],"experimental":[79],"structures":[80,104],"for":[81,90,114,122],"both":[82],"wild-type":[84],"mutant":[87],"unavailable":[89],"comparison.":[91],"With":[92],"MicroMiner,":[93],"we":[94,160],"extracted":[95,143],"$>255":[96],"\\times":[97,119],"10^{6}$":[98,120],"amino":[99],"acid":[100],"pairs":[101,121,145],"from":[105],"PDB,":[107],"exemplifying":[108],"single":[109,115],"mutations'":[110],"changes":[113],"chains":[116],"$>45":[118],"protein-protein":[123],"interfaces.":[124],"further":[126],"annotate":[127],"existing":[128],"sets":[130],"experimentally":[132],"measured":[133],"effects,":[135],"like":[136],"$\\Delta":[137],"\\Delta":[138],"G$":[139],"measurements,":[140],"with":[141,152],"combine":[147],"effect":[150],"measurement":[151],"change":[155],"upon":[156],"mutation.":[157],"In":[158],"addition,":[159],"show":[161],"how":[162],"can":[164],"bridge":[165],"gap":[167],"between":[168],"analysis":[170],"structure-based":[172],"drug":[173],"design":[174],"tools.":[175],"is":[177],"as":[179],"command":[181],"line":[182],"interactively":[185],"https://proteins.plus/":[188],"webserver.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}