{"id":"https://openalex.org/W1876226381","doi":"https://doi.org/10.1186/1758-2946-5-s1-p29","title":"Extended graph-based models for enhanced similarity retrieval in Cavbase","display_name":"Extended graph-based models for enhanced similarity retrieval in Cavbase","publication_year":2013,"publication_date":"2013-03-01","ids":{"openalex":"https://openalex.org/W1876226381","doi":"https://doi.org/10.1186/1758-2946-5-s1-p29","mag":"1876226381"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-s1-p29","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p29","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P29","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P29","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073954945","display_name":"Timo Krotzky","orcid":null},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Timo Krotzky","raw_affiliation_strings":["Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, Marburg/Lahn, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019483146","display_name":"Thomas Fober","orcid":null},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Fober","raw_affiliation_strings":["Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, Marburg/Lahn, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065824482","display_name":"Marco Mernberger","orcid":null},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marco Mernberger","raw_affiliation_strings":["Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, Marburg/Lahn, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005420915","display_name":"G. Klebe","orcid":"https://orcid.org/0000-0002-4913-390X"},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gerhard Klebe","raw_affiliation_strings":["Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, Marburg/Lahn, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Institute of Pharmaceutical Chemistry, Philipps-Universit\u00e4t, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059439673","display_name":"Eyke H\u00fcllermeier","orcid":"https://orcid.org/0000-0002-9944-4108"},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Eyke H\u00fcllermeier","raw_affiliation_strings":["Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, Marburg/Lahn, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, 35032, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Institute of Mathematics and Computer Science, Philipps-Universit\u00e4t, Marburg/Lahn, Germany","institution_ids":["https://openalex.org/I161103922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5073954945"],"corresponding_institution_ids":["https://openalex.org/I161103922"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.0464591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"5","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9943000078201294,"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":0.9943000078201294,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.992900013923645,"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":0.9907000064849854,"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/computer-science","display_name":"Computer science","score":0.7218879461288452},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.561522901058197},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5562072396278381},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5267809629440308},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.5217191576957703},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4873846173286438},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4869788587093353},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4720607399940491},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36286622285842896},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27176231145858765}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7218879461288452},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.561522901058197},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5562072396278381},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5267809629440308},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.5217191576957703},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4873846173286438},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4869788587093353},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4720607399940491},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36286622285842896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27176231145858765},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1758-2946-5-s1-p29","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p29","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P29","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2605457","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3606173","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"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-5-s1-p29","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p29","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P29","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1876226381.pdf","grobid_xml":"https://content.openalex.org/works/W1876226381.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W2031194866","https://openalex.org/W2146940292"],"related_works":["https://openalex.org/W2046435967","https://openalex.org/W4231775656","https://openalex.org/W2062195135","https://openalex.org/W2383646825","https://openalex.org/W2371018915","https://openalex.org/W2375480909","https://openalex.org/W2354191502","https://openalex.org/W2353314428","https://openalex.org/W2809157142","https://openalex.org/W2037023988"],"abstract_inverted_index":{"The":[0],"problem":[1],"of":[2,14,36,53,79,119,132,164,175,180,196,209,228,231,239],"estimating":[3],"the":[4,26,34,45,51,74,84,92,107,124,156,173,178,197,210,216,229,232],"similarity":[5,31],"between":[6,247],"molecular":[7,41,104],"structures":[8],"is":[9,135,172],"often":[10,151],"tackled":[11],"by":[12,138],"means":[13],"graph-based":[15,166],"approaches,":[16],"using":[17],"graphs":[18,46,195],"for":[19,73,243],"structure":[20],"representation":[21,111,118],"and":[22,77,115,241],"measures":[23,55],"based":[24,142,169],"on":[25,83,143,170],"maximum":[27],"common":[28],"subgraph":[29],"as":[30,40,226],"metrics.":[32],"In":[33,183],"case":[35],"protein":[37,85,181],"binding":[38,81,121],"sites":[39,82],"structures,":[42],"however,":[43,148],"where":[44],"can":[47],"be":[48],"very":[49,160],"large,":[50],"computation":[52],"these":[54],"may":[56],"easily":[57],"become":[58],"infeasible":[59],"or":[60],"at":[61],"least":[62],"unacceptably":[63],"slow.\r\n\r\nTo":[64],"this":[65,110,184],"end,":[66],"Cavbase":[67,87],"[1,2]":[68],"was":[69],"developed,":[70],"a":[71,120,130,165,237],"database":[72],"automatic":[75],"detection":[76],"storage":[78],"putative":[80],"surfaces.":[86],"assigns":[88],"so-called":[89],"pseudocenters":[90,171],"to":[91,103,113,194,236],"cavity-flanking":[93],"amino":[94],"acids,":[95],"which":[96,134,234],"characterize":[97],"their":[98],"physicochemical":[99],"properties":[100,223],"with":[101,129],"respect":[102],"recognition.":[105],"On":[106,123],"one":[108],"side,":[109,126],"leads":[112,193,235],"smaller":[114],"more":[116,203,244],"generic":[117],"site.":[122],"other":[125],"it":[127],"comes":[128],"loss":[131,174],"information,":[133],"usually":[136],"compensated":[137],"performing":[139],"further":[140],"calculations":[141],"additional":[144,207],"data.":[145],"These":[146,222],"steps,":[147],"are":[149,213,224],"most":[150],"computationally":[152],"quite":[153],"demanding,":[154],"making":[155],"whole":[157],"approach":[158],"again":[159],"slow.\r\n\r\nThe":[161],"main":[162],"drawback":[163],"model":[167],"solely":[168],"information":[176,240],"about":[177],"shape":[179],"surface.":[182],"study,":[185],"we":[186],"propose":[187],"an":[188],"extended":[189],"modeling":[190],"formalism":[191],"that":[192],"same":[198],"size,":[199],"but":[200],"containing":[201],"considerably":[202],"information.":[204],"More":[205],"specifically,":[206],"descriptors":[208],"surface":[211,217],"characteristics":[212],"extracted":[214],"from":[215],"points":[218],"stored":[219],"in":[220],"Cavbase.":[221],"included":[225],"attributes":[227],"nodes":[230],"graph,":[233],"gain":[238],"allows":[242],"accurate":[245],"comparisons":[246],"different":[248],"structures.":[249]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
