{"id":"https://openalex.org/W2131374321","doi":"https://doi.org/10.1145/974614.974655","title":"Mining protein family specific residue packing patterns from protein structure graphs","display_name":"Mining protein family specific residue packing patterns from protein structure graphs","publication_year":2004,"publication_date":"2004-01-01","ids":{"openalex":"https://openalex.org/W2131374321","doi":"https://doi.org/10.1145/974614.974655","mag":"2131374321"},"language":"en","primary_location":{"id":"doi:10.1145/974614.974655","is_oa":false,"landing_page_url":"https://doi.org/10.1145/974614.974655","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eighth annual international conference on Computational molecular biology  - RECOMB '04","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080409305","display_name":"Jun Huan","orcid":"https://orcid.org/0000-0002-7020-1604"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jun Huan","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052974651","display_name":"Deepak Bandyopadhyay","orcid":"https://orcid.org/0000-0002-8747-369X"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deepak Bandyopadhyay","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074061303","display_name":"Jack Snoeyink","orcid":"https://orcid.org/0000-0002-3887-4008"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack Snoeyink","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011567934","display_name":"Jan F. Prins","orcid":"https://orcid.org/0000-0003-0853-6099"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jan Prins","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078536199","display_name":"Alexander Tropsha","orcid":"https://orcid.org/0000-0003-3802-8896"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Tropsha","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5080409305"],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":null,"apc_paid":null,"fwci":18.5719,"has_fulltext":false,"cited_by_count":110,"citation_normalized_percentile":{"value":0.98907458,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"308","last_page":"315"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10538","display_name":"Data Mining Algorithms and Applications","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10538","display_name":"Data Mining Algorithms and Applications","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9940999746322632,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/delaunay-triangulation","display_name":"Delaunay triangulation","score":0.7825977206230164},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.5553730726242065},{"id":"https://openalex.org/keywords/vertex","display_name":"Vertex (graph theory)","score":0.5275523066520691},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4603677988052368},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.42990005016326904},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.36845099925994873},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.35345393419265747},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3367650508880615},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33604609966278076},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2668675184249878},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24677026271820068},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1718997359275818},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1466751992702484}],"concepts":[{"id":"https://openalex.org/C68010082","wikidata":"https://www.wikidata.org/wiki/Q192445","display_name":"Delaunay triangulation","level":2,"score":0.7825977206230164},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.5553730726242065},{"id":"https://openalex.org/C80899671","wikidata":"https://www.wikidata.org/wiki/Q1304193","display_name":"Vertex (graph theory)","level":3,"score":0.5275523066520691},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4603677988052368},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.42990005016326904},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36845099925994873},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.35345393419265747},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3367650508880615},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33604609966278076},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2668675184249878},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24677026271820068},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1718997359275818},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1466751992702484}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/974614.974655","is_oa":false,"landing_page_url":"https://doi.org/10.1145/974614.974655","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eighth annual international conference on Computational molecular biology  - RECOMB '04","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.183.2839","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.183.2839","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.duke.edu/%7Ebrd/Teaching/Bio/asmb/current/3papers/Bio/Design/tw-bw/p308-huan.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337397","display_name":"Division of Molecular and Cellular Biosciences","ror":"https://ror.org/002jdaq33"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1602224369","https://openalex.org/W1605903931","https://openalex.org/W1641749581","https://openalex.org/W1967390064","https://openalex.org/W1976373002","https://openalex.org/W1978036746","https://openalex.org/W1986969007","https://openalex.org/W1994058693","https://openalex.org/W2006927892","https://openalex.org/W2048792959","https://openalex.org/W2062351773","https://openalex.org/W2070143657","https://openalex.org/W2071818582","https://openalex.org/W2085277871","https://openalex.org/W2085673005","https://openalex.org/W2093547815","https://openalex.org/W2098853695","https://openalex.org/W2105187137","https://openalex.org/W2108797863","https://openalex.org/W2113712276","https://openalex.org/W2114370367","https://openalex.org/W2117019496","https://openalex.org/W2118349699","https://openalex.org/W2119148238","https://openalex.org/W2130179054","https://openalex.org/W2134861301","https://openalex.org/W2136593687","https://openalex.org/W2143513829","https://openalex.org/W2148603752","https://openalex.org/W2153504150","https://openalex.org/W2156909104","https://openalex.org/W2170726034","https://openalex.org/W2522853541","https://openalex.org/W2916193864","https://openalex.org/W3145128584","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2359979928","https://openalex.org/W2368353614","https://openalex.org/W2390369954","https://openalex.org/W1529719486","https://openalex.org/W2373917503","https://openalex.org/W2906423005","https://openalex.org/W4232052003","https://openalex.org/W2385297469","https://openalex.org/W2001914902","https://openalex.org/W2353399380"],"abstract_inverted_index":{"Finding":[0],"recurring":[1],"residue":[2],"packing":[3,112],"patterns,":[4],"or":[5],"spatial":[6,191],"motifs,":[7],"that":[8,166],"characterize":[9],"protein":[10,32,38,92,154,190],"structural":[11],"families":[12,137],"is":[13],"an":[14,43],"important":[15],"problem":[16],"in":[17,115,120,133,141],"bioinformatics.":[18],"We":[19,123],"apply":[20],"a":[21,40,80,86,91,142],"novel":[22],"frequent":[23,81],"subgraph":[24,82],"mining":[25,83,189],"algorithm":[26,84],"to":[27,85,110],"three":[28,52],"graph":[29],"representations":[30],"of":[31,88,98,118,128,151],"three-dimensional":[33],"(3D)":[34],"structure.":[35],"In":[36],"each":[37],"graph,":[39],"vertex":[41],"represents":[42],"amino":[44],"acid.":[45],"Vertex-residues":[46],"are":[47,149,175,184],"connected":[48],"by":[49],"edges":[50],"using":[51,64,73],"approaches:":[53],"first,":[54],"based":[55,168],"on":[56,169],"simple":[57],"distance":[58,180],"threshold":[59],"between":[60],"contact":[61,179],"residues;":[62],"second":[63],"the":[65,74,95,116,121,126,153,158,178],"Delaunay":[66,173],"tessellation":[67,78],"from":[68,94,131],"computational":[69],"geometry,":[70],"and":[71,172,186],"third":[72],"recently":[75],"developed":[76],"almost-Delaunay":[77,171],"approach.Applying":[79],"set":[87],"graphs":[89,167],"representing":[90],"family":[93,155],"Structural":[96],"Classification":[97],"Proteins":[99],"(SCOP)":[100],"database,":[101],"we":[102],"typically":[103],"identify":[104],"several":[105],"hundred":[106],"common":[107,111],"subgraphs":[108],"equivalent":[109],"motifs":[113,129],"found":[114],"majority":[117],"proteins":[119,132],"family.":[122],"also":[124],"use":[125],"counts":[127],"extracted":[130],"two":[134],"different":[135],"SCOP":[136],"as":[138],"input":[139],"variables":[140],"binary":[143],"classification":[144],"experiment.":[145],"The":[146],"resulting":[147],"models":[148],"capable":[150],"predicting":[152],"association":[156],"with":[157],"accuracy":[159],"exceeding":[160],"90":[161],"percent.":[162],"Our":[163],"results":[164],"indicate":[165],"both":[170],"tessellations":[174],"sparser":[176],"than":[177],"graphs;":[181],"yet":[182],"they":[183],"robust":[185],"efficient":[187],"for":[188],"motif.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}