{"id":"https://openalex.org/W1883316518","doi":"https://doi.org/10.1186/s12859-015-0776-9","title":"PDB-Explorer: a web-based interactive map of the protein data bank in shape space","display_name":"PDB-Explorer: a web-based interactive map of the protein data bank in shape space","publication_year":2015,"publication_date":"2015-10-23","ids":{"openalex":"https://openalex.org/W1883316518","doi":"https://doi.org/10.1186/s12859-015-0776-9","mag":"1883316518","pmid":"https://pubmed.ncbi.nlm.nih.gov/26493835"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0776-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0776-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0776-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0776-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049987748","display_name":"Xian Jin","orcid":"https://orcid.org/0000-0001-8002-3111"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Xian Jin","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland. xian.jin@dcb.unibe.ch","Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland. xian.jin@dcb.unibe.ch","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004141939","display_name":"Mahendra Awale","orcid":"https://orcid.org/0000-0002-0611-6552"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mahendra Awale","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland. mahendra.awale@dcb.unibe.ch","Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland. mahendra.awale@dcb.unibe.ch","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013402673","display_name":"Micha\u00ebl Zasso","orcid":"https://orcid.org/0000-0001-5295-2159"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Micha\u00ebl Zasso","raw_affiliation_strings":["Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland. mic.besace@gmail.com","Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC),Lausanne,Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland. mic.besace@gmail.com","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC),Lausanne,Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061436114","display_name":"Daniel Kostro","orcid":null},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Daniel Kostro","raw_affiliation_strings":["Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland. kostro.d@gmail.com","Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC),Lausanne,Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland. kostro.d@gmail.com","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC),Lausanne,Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064912268","display_name":"Luc Patiny","orcid":"https://orcid.org/0000-0002-4943-2643"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Luc Patiny","raw_affiliation_strings":["Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland. luc.patiny@epfl.ch","Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC),Lausanne,Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Lausanne, 1015, Switzerland. luc.patiny@epfl.ch","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC),Lausanne,Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040848839","display_name":"Jean\u2010Louis Reymond","orcid":"https://orcid.org/0000-0003-2724-2942"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Jean-Louis Reymond","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland. jean-louis.reymond@dcb.unibe.ch","Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012, Berne, Switzerland. jean-louis.reymond@dcb.unibe.ch","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5040848839"],"corresponding_institution_ids":["https://openalex.org/I118564535"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1593,"currency":"EUR","value_usd":1718},"fwci":1.5447,"has_fulltext":true,"cited_by_count":46,"citation_normalized_percentile":{"value":0.81318321,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"339","last_page":"339"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.7912999987602234,"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":0.7912999987602234,"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":0.09109999984502792,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.013799999840557575,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer 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":0.8317275047302246},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6453517079353333},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5247064828872681},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.46614280343055725},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4505109488964081},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.431590735912323},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3481508493423462},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33855342864990234},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.20556801557540894}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8317275047302246},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6453517079353333},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5247064828872681},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.46614280343055725},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4505109488964081},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.431590735912323},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3481508493423462},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33855342864990234},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.20556801557540894},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-015-0776-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0776-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0776-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26493835","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26493835","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:boris.unibe.ch:74705","is_oa":true,"landing_page_url":"https://boris.unibe.ch/74705/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401086","display_name":"Bern Open Repository and Information System (University of Bern)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118564535","host_organization_name":"University of Bern","host_organization_lineage":["https://openalex.org/I118564535"],"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":"Jin, Xian; Awale, Mahendra; Zasso, Micha\u00ebl; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis (2015). PDB-Explorer: a web-based interactive map of the protein data bank in shape space. BMC bioinformatics, 16(1), 16:339. BioMed Central 10.1186/s12859-015-0776-9 &lt;http://dx.doi.org/10.1186/s12859-015-0776-9&gt;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:3588073","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4619230","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:infoscience.epfl.ch:214015","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/214015","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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:10.1186/s12859-015-0776-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0776-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0776-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1385680656","display_name":null,"funder_award_id":"200020_159941","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1883316518.pdf","grobid_xml":"https://content.openalex.org/works/W1883316518.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W986143497","https://openalex.org/W1966613725","https://openalex.org/W1966679395","https://openalex.org/W1967538863","https://openalex.org/W1968278549","https://openalex.org/W1975369978","https://openalex.org/W1978113501","https://openalex.org/W1979439052","https://openalex.org/W1980663085","https://openalex.org/W1992156271","https://openalex.org/W1993560924","https://openalex.org/W2001424887","https://openalex.org/W2021748110","https://openalex.org/W2025088751","https://openalex.org/W2026421403","https://openalex.org/W2026909852","https://openalex.org/W2027482274","https://openalex.org/W2029579649","https://openalex.org/W2030517878","https://openalex.org/W2031372687","https://openalex.org/W2035503835","https://openalex.org/W2038671703","https://openalex.org/W2042732542","https://openalex.org/W2047847505","https://openalex.org/W2048947602","https://openalex.org/W2055925492","https://openalex.org/W2057069307","https://openalex.org/W2065794506","https://openalex.org/W2067852761","https://openalex.org/W2067868112","https://openalex.org/W2070741080","https://openalex.org/W2074235299","https://openalex.org/W2091155135","https://openalex.org/W2091275638","https://openalex.org/W2091506983","https://openalex.org/W2092493635","https://openalex.org/W2096541451","https://openalex.org/W2097632784","https://openalex.org/W2102245393","https://openalex.org/W2103148772","https://openalex.org/W2105254477","https://openalex.org/W2105869636","https://openalex.org/W2106531843","https://openalex.org/W2108067237","https://openalex.org/W2110818745","https://openalex.org/W2114459720","https://openalex.org/W2118233996","https://openalex.org/W2122326469","https://openalex.org/W2126103104","https://openalex.org/W2128653811","https://openalex.org/W2130629641","https://openalex.org/W2134815007","https://openalex.org/W2141528038","https://openalex.org/W2152326664","https://openalex.org/W2153228625","https://openalex.org/W2157122545","https://openalex.org/W2168667184","https://openalex.org/W2168708922","https://openalex.org/W2169395813","https://openalex.org/W2171681733","https://openalex.org/W2197008132","https://openalex.org/W3149078497","https://openalex.org/W4234914623","https://openalex.org/W4255594044"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W2090630809","https://openalex.org/W2106612397","https://openalex.org/W4387804157","https://openalex.org/W2518314460","https://openalex.org/W2589205199","https://openalex.org/W2119891507","https://openalex.org/W2089869950","https://openalex.org/W2047544230"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,107,122,184,237,310],"RCSB":[2],"Protein":[3],"Data":[4],"Bank":[5],"(PDB)":[6],"provides":[7,245],"public":[8],"access":[9,33],"to":[10,27,32,43,71,89,97,113,132,140,248,323],"experimentally":[11],"determined":[12],"3D-structures":[13],"of":[14,38,76,87,117,158,164,192,196,250,271,299,331],"biological":[15],"macromolecules":[16],"(proteins,":[17],"peptides":[18,96],"and":[19,42,99,128,217,234,255,286,304,318,326],"nucleic":[20],"acids).":[21],"While":[22],"various":[23],"tools":[24],"are":[25,173,209],"available":[26,315],"explore":[28,327],"the":[29,34,39,73,85,115,165,180,207,228,243,260,300,328,332],"PDB,":[30],"options":[31],"global":[35],"structural":[36,329],"diversity":[37,330],"entire":[40],"PDB":[41,47,118,159,202,230,272,301],"perceive":[44],"relationships":[45],"between":[46,142],"structures":[48],"remain":[49],"very":[50],"limited.":[51],"METHODS:":[52],"A":[53,267],"136-dimensional":[54],"atom":[55,63],"pair":[56],"3D-fingerprint":[57,283],"for":[58,284],"proteins":[59,127,258,285],"(3DP)":[60],"counting":[61],"categorized":[62],"pairs":[64],"at":[65,316],"increasing":[66],"through-space":[67],"distances":[68],"was":[69,111,277],"designed":[70],"represent":[72],"molecular":[74,275],"shape":[75,276],"PDB-entries.":[77],"Nearest":[78],"neighbor":[79,190,307],"searches":[80,191],"examples":[81],"were":[82],"reported":[83],"exemplifying":[84],"ability":[86,139],"3DP-similarity":[88,240],"identify":[90],"closely":[91,143],"related":[92,144],"biomolecules":[93],"from":[94,220,259],"small":[95],"enzyme":[98],"large":[100],"multiprotein":[101],"complexes":[102],"such":[103],"as":[104,176,200],"virus":[105],"particles.":[106],"principle":[108],"component":[109],"analysis":[110],"used":[112],"obtain":[114],"visualization":[116],"in":[119,160,211,213,263,288],"3DP-space.":[120,161],"RESULTS:":[121],"3DP":[123],"property":[124],"space":[125,269,303],"groups":[126],"protein":[129],"assemblies":[130],"according":[131],"their":[133],"3D-shape":[134],"similarity,":[135],"yet":[136],"shows":[137],"exquisite":[138],"distinguish":[141],"structures.":[145],"An":[146],"interactive":[147,156,296],"website":[148,186,208,312],"called":[149],"PDB-Explorer":[150,185,244,311],"is":[151,182,224,313],"presented":[152],"featuring":[153],"a":[154,214,221,280,289,305],"color-coded":[155,297],"map":[157,166,298],"Each":[162],"pixel":[163,181],"contains":[167],"one":[168],"or":[169,195],"more":[170],"PDB-entries":[171],"which":[172],"directly":[174],"visualized":[175],"ribbon":[177],"diagrams":[178],"when":[179],"selected.":[183],"allows":[187],"performing":[188],"3DP-nearest":[189],"any":[193,197],"PDB-entry":[194],"structure":[198],"uploaded":[199],"protein-type":[201],"file.":[203],"All":[204],"functionalities":[205],"on":[206,274],"implemented":[210,287],"JavaScript":[212],"platform-independent":[215],"manner":[216],"draw":[218],"data":[219],"server":[222],"that":[223],"updated":[225],"daily":[226],"with":[227,242],"latest":[229],"additions,":[231],"ensuring":[232],"complete":[233],"up-to-date":[235],"coverage.":[236],"essentially":[238],"instantaneous":[239],"search":[241,308],"results":[246],"comparable":[247],"those":[249],"much":[251],"slower":[252],"3D-alignment":[253],"algorithms,":[254],"automatically":[256],"clusters":[257],"same":[261],"superfamilies":[262],"tight":[264],"groups.":[265],"CONCLUSION:":[266],"chemical":[268,302],"classification":[270],"based":[273],"obtained":[278],"using":[279],"new":[281],"atom-pair":[282],"web-based":[290],"database":[291],"exploration":[292],"tool":[293],"comprising":[294],"an":[295,320],"nearest":[306],"tool.":[309],"freely":[314],"www.cheminfo.org/pdbexplorer":[317],"represents":[319],"unprecedented":[321],"opportunity":[322],"interactively":[324],"visualize":[325],"PDB.":[333],"\u115f":[334]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2025-10-10T00:00:00"}
