{"id":"https://openalex.org/W2036106789","doi":"https://doi.org/10.1093/bioinformatics/btg343","title":"Accelerating screening of 3D protein data with a graph theoretical approach","display_name":"Accelerating screening of 3D protein data with a graph theoretical approach","publication_year":2003,"publication_date":"2003-12-10","ids":{"openalex":"https://openalex.org/W2036106789","doi":"https://doi.org/10.1093/bioinformatics/btg343","mag":"2036106789","pmid":"https://pubmed.ncbi.nlm.nih.gov/14668229"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg343","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg343","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112588600","display_name":"Cornelius Fr\u00f6mmel","orcid":null},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Cornelius Fr\u00f6mmel","raw_affiliation_strings":["Institut f\u00fcr Biochemie, Charit\u00e9, Monbijoustr. 2, Berlin, D-10117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Biochemie, Charit\u00e9, Monbijoustr. 2, Berlin, D-10117, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040090614","display_name":"Christoph Gille","orcid":null},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christoph Gille","raw_affiliation_strings":["Charite"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charite","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062823306","display_name":"Andrean Goede","orcid":"https://orcid.org/0000-0002-9044-9869"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrean Goede","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059596381","display_name":"Clemens Gr\u00f6pl","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Clemens Gr\u00f6pl","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085228445","display_name":"Stefan Hougardy","orcid":"https://orcid.org/0000-0001-8656-3418"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stefan Hougardy","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026515787","display_name":"Till Nierhoff","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Till Nierhoff","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043414157","display_name":"Robert Prei\u00dfner","orcid":"https://orcid.org/0000-0002-2407-1087"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert Prei\u00dfner","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5080881773","display_name":"Martin Thimm","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martin Thimm","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5112588600"],"corresponding_institution_ids":["https://openalex.org/I7877124"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9163,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.71889643,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"18","first_page":"2442","last_page":"2447"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6908000111579895,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6908000111579895,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.11969999969005585,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.051899999380111694,"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/traverse","display_name":"Traverse","score":0.8273876905441284},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7377427220344543},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6947124004364014},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6086601614952087},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5487322807312012},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42669692635536194},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4240814447402954},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.41867882013320923},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.333553671836853},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3218245506286621},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2900448143482208},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.1497383713722229}],"concepts":[{"id":"https://openalex.org/C176809094","wikidata":"https://www.wikidata.org/wiki/Q15401496","display_name":"Traverse","level":2,"score":0.8273876905441284},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7377427220344543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6947124004364014},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6086601614952087},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5487322807312012},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42669692635536194},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4240814447402954},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.41867882013320923},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.333553671836853},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3218245506286621},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2900448143482208},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.1497383713722229},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","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":"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/btg343","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg343","pdf_url":null,"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:14668229","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14668229","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:CiteSeerX.psu:10.1.1.4.9398","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.4.9398","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.informatik.hu-berlin.de/~hougardy/paper/cl12.ps","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W19883518","https://openalex.org/W1540930565","https://openalex.org/W1541165771","https://openalex.org/W1972935024","https://openalex.org/W1980593789","https://openalex.org/W1985255401","https://openalex.org/W2011248912","https://openalex.org/W2031372687","https://openalex.org/W2036034114","https://openalex.org/W2050032036","https://openalex.org/W2054145937","https://openalex.org/W2065183358","https://openalex.org/W2070942956","https://openalex.org/W2075900721","https://openalex.org/W2077990749","https://openalex.org/W2092420654","https://openalex.org/W2092802075","https://openalex.org/W2093416767","https://openalex.org/W2096729078","https://openalex.org/W2128727994","https://openalex.org/W2132603077","https://openalex.org/W2176645417","https://openalex.org/W2327127510","https://openalex.org/W2412152270","https://openalex.org/W2444554091","https://openalex.org/W2905110430"],"related_works":["https://openalex.org/W2377402383","https://openalex.org/W2380835401","https://openalex.org/W2381912691","https://openalex.org/W2350381577","https://openalex.org/W2353618196","https://openalex.org/W2348074676","https://openalex.org/W2354294614","https://openalex.org/W2354191910","https://openalex.org/W4241574154","https://openalex.org/W2536030737"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,40,86,103],"Dictionary":[2],"of":[3,15,18,42,45,66,84,94,97,100,109,124,146,149,156,188],"Interfaces":[4],"in":[5,29,159],"Proteins":[6],"(DIP)":[7],"is":[8,48],"a":[9,27,72,81,144,174,186,194],"database":[10],"collecting":[11],"the":[12,43,53,64,68,92,95,98,107,128,133,147,157,168],"3D":[13],"structure":[14],"interacting":[16],"parts":[17],"proteins":[19],"that":[20,119],"are":[21],"called":[22],"patches.":[23,101],"It":[24],"serves":[25],"as":[26],"repository,":[28],"which":[30],"patches":[31,36,47,69,111,171,181],"similar":[32,70,172,180],"to":[33,71,88,121,165,173],"given":[34,73,175],"query":[35,74],"can":[37,75,112,136,162],"be":[38,76,114,137,163,183,198],"found.":[39],"computation":[41],"similarity":[44,99,108,196],"two":[46,110,129,140],"time":[49],"consuming":[50],"and":[51],"traversing":[52],"entire":[54],"DIP":[55,169],"requires":[56,91],"some":[57],"hours.":[58],"In":[59],"this":[60,89],"work":[61],"we":[62],"address":[63],"question":[65,90],"how":[67],"identified":[77],"by":[78,139,185,204],"scanning":[79,167],"only":[80],"small":[82],"part":[83],"DIP.":[85,160],"answer":[87],"investigation":[93],"distribution":[96],"RESULTS:":[102],"score":[104],"values":[105],"describing":[106],"roughly":[113],"divided":[115],"into":[116],"three":[117,134],"ranges":[118],"correspond":[120],"different":[122,141],"levels":[123],"spatial":[125],"similarity.":[126],"Interestingly,":[127],"iso-score":[130],"lines":[131],"separating":[132],"classes":[135],"determined":[138],"approaches.":[142],"Applying":[143],"concept":[145],"theory":[148],"random":[150],"graphs":[151],"reveals":[152],"significant":[153],"structural":[154],"properties":[155],"data":[158],"These":[161],"used":[164],"accelerate":[166],"for":[170,178],"query.":[176],"Searches":[177],"very":[179],"could":[182,197],"accelerated":[184],"factor":[187],"more":[189],"than":[190,203],"25.":[191],"Patches":[192],"with":[193],"medium":[195],"found":[199],"10":[200],"times":[201],"faster":[202],"brute-force":[205],"search.":[206]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}