{"id":"https://openalex.org/W2124973646","doi":"https://doi.org/10.1093/bioinformatics/bth106","title":"Using convex hulls to extract interaction interfaces from known structures","display_name":"Using convex hulls to extract interaction interfaces from known structures","publication_year":2004,"publication_date":"2004-07-01","ids":{"openalex":"https://openalex.org/W2124973646","doi":"https://doi.org/10.1093/bioinformatics/bth106","mag":"2124973646","pmid":"https://pubmed.ncbi.nlm.nih.gov/15231539"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth106","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/10/1486/48905948/bioinformatics_20_10_1486.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/20/10/1486/48905948/bioinformatics_20_10_1486.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034739719","display_name":"Panos Dafas","orcid":null},"institutions":[{"id":"https://openalex.org/I180825142","display_name":"City, University of London","ror":"https://ror.org/04489at23","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I180825142"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Panos Dafas","raw_affiliation_strings":["Department of Computing, City University, London, EC1V 0HB, UK. panos@alumni.doc.ic.ac.uk","Department of Computing, City University, London EC1V 0HB, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computing, City University, London, EC1V 0HB, UK. panos@alumni.doc.ic.ac.uk","institution_ids":["https://openalex.org/I180825142"]},{"raw_affiliation_string":"Department of Computing, City University, London EC1V 0HB, UK","institution_ids":["https://openalex.org/I180825142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005347238","display_name":"Dan Bolser","orcid":"https://orcid.org/0000-0002-3991-0859"},"institutions":[{"id":"https://openalex.org/I90344618","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517","country_code":"GB","type":"funder","lineage":["https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Dan Bolser","raw_affiliation_strings":["Medical Research Council, Dunn Human Nutrition Unit, Cambridge, CB2 2QH, UK,#TAB#"],"affiliations":[{"raw_affiliation_string":"Medical Research Council, Dunn Human Nutrition Unit, Cambridge, CB2 2QH, UK,#TAB#","institution_ids":["https://openalex.org/I90344618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050095820","display_name":"Jacek Gomoluch","orcid":null},"institutions":[{"id":"https://openalex.org/I180825142","display_name":"City, University of London","ror":"https://ror.org/04489at23","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I180825142"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jacek Gomoluch","raw_affiliation_strings":["Department of Computing, City University, London EC1V 0HB, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computing, City University, London EC1V 0HB, UK","institution_ids":["https://openalex.org/I180825142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100678933","display_name":"Jong Moon Park","orcid":"https://orcid.org/0000-0002-5852-3475"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jong Park","raw_affiliation_strings":["Biomatics Lab, BioSystems Department, DaeJeon, KAIST, Korea#TAB#"],"affiliations":[{"raw_affiliation_string":"Biomatics Lab, BioSystems Department, DaeJeon, KAIST, Korea#TAB#","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016411406","display_name":"Michael Schroeder","orcid":"https://orcid.org/0000-0003-2848-6949"},"institutions":[{"id":"https://openalex.org/I180825142","display_name":"City, University of London","ror":"https://ror.org/04489at23","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I180825142"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael Schroeder","raw_affiliation_strings":["Department of Computing, City University, London EC1V 0HB, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computing, City University, London EC1V 0HB, UK","institution_ids":["https://openalex.org/I180825142"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5034739719"],"corresponding_institution_ids":["https://openalex.org/I180825142"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5202,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.81155057,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"10","first_page":"1486","last_page":"1490"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9950000047683716,"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":0.9950000047683716,"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/T10260","display_name":"Software Engineering Research","score":0.9664999842643738,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.963699996471405,"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/hull","display_name":"Hull","score":0.6976978182792664},{"id":"https://openalex.org/keywords/convex-hull","display_name":"Convex hull","score":0.6888405680656433},{"id":"https://openalex.org/keywords/regular-polygon","display_name":"Regular polygon","score":0.5886309742927551},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49244365096092224},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3509923219680786},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3358754515647888},{"id":"https://openalex.org/keywords/composite-material","display_name":"Composite material","score":0.1533004343509674},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.15179020166397095},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.14849990606307983}],"concepts":[{"id":"https://openalex.org/C37423430","wikidata":"https://www.wikidata.org/wiki/Q6750281","display_name":"Hull","level":2,"score":0.6976978182792664},{"id":"https://openalex.org/C206194317","wikidata":"https://www.wikidata.org/wiki/Q1138624","display_name":"Convex hull","level":3,"score":0.6888405680656433},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.5886309742927551},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49244365096092224},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3509923219680786},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3358754515647888},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.1533004343509674},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.15179020166397095},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.14849990606307983}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth106","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/10/1486/48905948/bioinformatics_20_10_1486.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:15231539","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15231539","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:scholarworks.unist.ac.kr:201301/13208","is_oa":false,"landing_page_url":"https://scholarworks.unist.ac.kr/handle/201301/13208","pdf_url":null,"source":{"id":"https://openalex.org/S4306401118","display_name":"Scholarworks@UNIST (Ulsan National Institute of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I48566637","host_organization_name":"Ulsan National Institute of Science and Technology","host_organization_lineage":["https://openalex.org/I48566637"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"ARTICLE"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth106","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth106","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/10/1486/48905948/bioinformatics_20_10_1486.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":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2124973646.pdf","grobid_xml":"https://content.openalex.org/works/W2124973646.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W115622331","https://openalex.org/W2041775009","https://openalex.org/W2085277871","https://openalex.org/W2130479394","https://openalex.org/W2144231753"],"related_works":["https://openalex.org/W2467926385","https://openalex.org/W2893068807","https://openalex.org/W161301265","https://openalex.org/W2483619716","https://openalex.org/W4246461909","https://openalex.org/W2377576908","https://openalex.org/W2971424936","https://openalex.org/W2007256320","https://openalex.org/W2991249704","https://openalex.org/W563487689"],"abstract_inverted_index":{"We":[0],"address":[1],"these":[2],"two":[3],"shortcomings":[4],"by":[5,44],"developing":[6],"a":[7,45,56,64],"family":[8],"of":[9,15,22,35,47,66,87],"new":[10,72,93],"algorithms":[11,37,54,73],"for":[12],"the":[13,20,30,36,40,50,53,71,75,92,100],"computation":[14,76],"domain-domain":[16],"interactions":[17],"based":[18],"on":[19,39,49,63],"idea":[21],"bounding":[23],"shapes,":[24],"which":[25,59],"are":[26],"used":[27],"to":[28,82],"prune":[29],"search":[31],"space.":[32],"The":[33,85],"best":[34],"improves":[38],"old":[41],"PSIMAP":[42],"algorithm":[43,94],"factor":[46],"60":[48],"PDB.":[51,104],"Additionally,":[52],"allow":[55],"distributed":[57],"computation,":[58],"we":[60],"carry":[61],"out":[62],"farm":[65],"80":[67],"Linux":[68],"PCs.":[69],"Overall,":[70],"reduce":[74],"at":[77],"atomic":[78],"level":[79],"from":[80],"months":[81],"20":[83],"min.":[84],"combination":[86],"pruning":[88],"and":[89,96],"distribution":[90],"makes":[91],"scalable":[95],"sustainable":[97],"even":[98],"with":[99],"superlinear":[101],"growth":[102],"in":[103]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}