{"id":"https://openalex.org/W2140468273","doi":"https://doi.org/10.1093/bioinformatics/btq573","title":"Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure","display_name":"Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure","publication_year":2010,"publication_date":"2010-11-02","ids":{"openalex":"https://openalex.org/W2140468273","doi":"https://doi.org/10.1093/bioinformatics/btq573","mag":"2140468273","pmid":"https://pubmed.ncbi.nlm.nih.gov/21047817"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3059/16896529/btq573.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3059/16896529/btq573.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102951410","display_name":"Ryan Day","orcid":"https://orcid.org/0000-0002-7777-2100"},"institutions":[{"id":"https://openalex.org/I119942576","display_name":"University of the Pacific","ror":"https://ror.org/05ma4gw77","country_code":"US","type":"education","lineage":["https://openalex.org/I119942576"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Day","raw_affiliation_strings":["1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA","institution_ids":["https://openalex.org/I119942576","https://openalex.org/I91045830","https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089541569","display_name":"Kristin P. Lennox","orcid":null},"institutions":[{"id":"https://openalex.org/I119942576","display_name":"University of the Pacific","ror":"https://ror.org/05ma4gw77","country_code":"US","type":"education","lineage":["https://openalex.org/I119942576"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristin P. Lennox","raw_affiliation_strings":["1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA","institution_ids":["https://openalex.org/I119942576","https://openalex.org/I91045830","https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077993349","display_name":"David B. Dahl","orcid":"https://orcid.org/0000-0002-8173-1547"},"institutions":[{"id":"https://openalex.org/I119942576","display_name":"University of the Pacific","ror":"https://ror.org/05ma4gw77","country_code":"US","type":"education","lineage":["https://openalex.org/I119942576"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David B. Dahl","raw_affiliation_strings":["1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA","institution_ids":["https://openalex.org/I119942576","https://openalex.org/I91045830","https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030348494","display_name":"Marina Vannucci","orcid":"https://orcid.org/0000-0002-7360-5321"},"institutions":[{"id":"https://openalex.org/I119942576","display_name":"University of the Pacific","ror":"https://ror.org/05ma4gw77","country_code":"US","type":"education","lineage":["https://openalex.org/I119942576"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marina Vannucci","raw_affiliation_strings":["1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA","institution_ids":["https://openalex.org/I119942576","https://openalex.org/I91045830","https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044318747","display_name":"Jerry Tsai","orcid":"https://orcid.org/0000-0001-9752-9223"},"institutions":[{"id":"https://openalex.org/I119942576","display_name":"University of the Pacific","ror":"https://ror.org/05ma4gw77","country_code":"US","type":"education","lineage":["https://openalex.org/I119942576"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jerry W. Tsai","raw_affiliation_strings":["1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Chemistry, University of the Pacific, Stockton, CA 95211, 2Department of Statistics, Texas A&M University, College Station, TX 77843 and 3Department of Statistics, Rice University, Houston, TX 77251, USA","institution_ids":["https://openalex.org/I119942576","https://openalex.org/I91045830","https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4084,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.64079705,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"26","issue":"24","first_page":"3059","last_page":"3066"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8608999848365784,"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":0.8608999848365784,"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":0.07639999687671661,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.007300000172108412,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"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/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.6980633735656738},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5213919281959534},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.48952993750572205},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.46671077609062195},{"id":"https://openalex.org/keywords/tetrahedron","display_name":"Tetrahedron","score":0.4659709930419922},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.4265105426311493},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3578784465789795},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2225627899169922},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.2104024887084961},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.20500153303146362},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1354033350944519},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.09940925240516663}],"concepts":[{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.6980633735656738},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5213919281959534},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.48952993750572205},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.46671077609062195},{"id":"https://openalex.org/C105239961","wikidata":"https://www.wikidata.org/wiki/Q160003","display_name":"Tetrahedron","level":2,"score":0.4659709930419922},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.4265105426311493},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3578784465789795},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2225627899169922},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.2104024887084961},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.20500153303146362},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1354033350944519},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.09940925240516663},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3059/16896529/btq573.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21047817","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21047817","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:pubmedcentral.nih.gov:2995117","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2995117","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/24/3059/16896529/btq573.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1520127302","https://openalex.org/W1966388405","https://openalex.org/W1969644422","https://openalex.org/W1974138195","https://openalex.org/W1976287380","https://openalex.org/W1986969007","https://openalex.org/W1988044901","https://openalex.org/W1991019032","https://openalex.org/W1998452873","https://openalex.org/W1998931880","https://openalex.org/W2004461664","https://openalex.org/W2006481713","https://openalex.org/W2013823922","https://openalex.org/W2014376206","https://openalex.org/W2016598344","https://openalex.org/W2019333687","https://openalex.org/W2019866342","https://openalex.org/W2048918663","https://openalex.org/W2049902088","https://openalex.org/W2050425137","https://openalex.org/W2051895548","https://openalex.org/W2053803268","https://openalex.org/W2062926294","https://openalex.org/W2070571039","https://openalex.org/W2073112694","https://openalex.org/W2077752734","https://openalex.org/W2085277871","https://openalex.org/W2086473602","https://openalex.org/W2089597488","https://openalex.org/W2091114929","https://openalex.org/W2092598726","https://openalex.org/W2093937568","https://openalex.org/W2098084175","https://openalex.org/W2101298197","https://openalex.org/W2101449937","https://openalex.org/W2104497506","https://openalex.org/W2116007667","https://openalex.org/W2118347512","https://openalex.org/W2124117395","https://openalex.org/W2126016150","https://openalex.org/W2130179054","https://openalex.org/W2132653593","https://openalex.org/W2132926880","https://openalex.org/W2133657429","https://openalex.org/W2135815512","https://openalex.org/W2139433006","https://openalex.org/W2139445777","https://openalex.org/W2145045494","https://openalex.org/W2150627302","https://openalex.org/W2160336700","https://openalex.org/W2160888224","https://openalex.org/W2165085526","https://openalex.org/W2170512042","https://openalex.org/W2171755502","https://openalex.org/W2171962405","https://openalex.org/W2426438071","https://openalex.org/W2611034874","https://openalex.org/W6644525740"],"related_works":["https://openalex.org/W2090630809","https://openalex.org/W2584773272","https://openalex.org/W2084743099","https://openalex.org/W2121688928","https://openalex.org/W4235583582","https://openalex.org/W1975453400","https://openalex.org/W1997379747","https://openalex.org/W2016543047","https://openalex.org/W2602307348","https://openalex.org/W2220384852"],"abstract_inverted_index":{"MOTIVATION:":[0],"While":[1],"protein":[2,161],"secondary":[3,164,184],"structure":[4,79,121],"is":[5,51,143],"well":[6],"understood,":[7],"representing":[8],"the":[9,25,32,44,67,115,128,226,236],"repetitive":[10,94],"nature":[11],"of":[12,56,77,96,102,118,132,149,225,235],"tertiary":[13,78,81,97,120],"packing":[14,27,45,142],"in":[15,47,122],"proteins":[16,170],"remains":[17],"difficult.":[18],"We":[19,166],"have":[20,212],"developed":[21,213],"a":[22,39,54,74,88,179],"construct":[23,86],"called":[24],"relative":[26],"group":[28],"(RPG)":[29],"that":[30,140,168],"applies":[31],"clique":[33,55],"concept":[34],"from":[35],"graph":[36],"theory":[37],"as":[38,53,64],"natural":[40],"basis":[41],"for":[42],"defining":[43],"motifs":[46],"proteins.":[48],"An":[49],"RPG":[50],"defined":[52],"residues,":[57,190,197],"where":[58],"every":[59],"member":[60],"contacts":[61],"all":[62],"others":[63],"determined":[65],"by":[66,183],"Delaunay":[68],"tessellation.":[69],"Geometrically":[70],"similar":[71,141],"RPGs":[72,107,150,172],"define":[73],"regular":[75,119],"element":[76],"or":[80],"motif":[82],"(TerMo).":[83],"This":[84],"intuitive":[85,217],"provides":[87],"simple":[89],"approach":[90],"to":[91,113,160],"characterize":[92,114],"general":[93],"elements":[95],"structure.":[98,165],"RESULTS:":[99],"A":[100],"dataset":[101],"over":[103],"4":[104],"million":[105],"tetrahedral":[106],"was":[108],"clustered":[109],"using":[110],"different":[111,146],"criteria":[112],"various":[116],"aspects":[117],"TerMos.":[123],"Grouping":[124],"this":[125],"data":[126],"within":[127],"SCOP":[129],"classification":[130],"levels":[131],"Family,":[133],"Superfamily,":[134],"Fold,":[135],"Class":[136],"and":[137,163,200,216,230,243],"PDB":[138],"showed":[139],"shared":[144],"across":[145],"folds.":[147],"Classification":[148],"based":[151],"on":[152],"residue":[153],"sequence":[154],"locality":[155],"reveals":[156],"topological":[157],"preferences":[158],"according":[159],"sizes":[162],"find":[167],"larger":[169],"favor":[171,192],"with":[173,203],"three":[174],"local":[175,189,196,205],"residues":[176],"packed":[177],"against":[178],"non-local":[180],"residue.":[181],"Classifying":[182],"structure,":[185],"helices":[186],"prefer":[187],"mostly":[188],"sheets":[191],"at":[193],"least":[194],"two":[195],"while":[198],"turns":[199],"coil":[201],"populate":[202],"more":[204],"residues.":[206],"To":[207],"depict":[208],"these":[209],"TerMos,":[210],"we":[211],"2":[214],"complementary":[215],"representations:":[218],"(i)":[219],"Dirichlet":[220],"process":[221],"mixture":[222],"density":[223,233],"estimation":[224,234],"torsion":[227],"angle":[228],"distributions":[229],"(ii)":[231],"kernel":[232],"Cartesian":[237],"coordinate":[238],"distribution.":[239],"The":[240],"TerMo":[241],"library":[242],"representations":[244],"software":[245],"are":[246],"available":[247],"upon":[248],"request.":[249]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
