{"id":"https://openalex.org/W2098423804","doi":"https://doi.org/10.1186/1758-2946-2-s1-p11","title":"Where are the boundaries? Automated pocket detection for druggability studies","display_name":"Where are the boundaries? Automated pocket detection for druggability studies","publication_year":2010,"publication_date":"2010-05-01","ids":{"openalex":"https://openalex.org/W2098423804","doi":"https://doi.org/10.1186/1758-2946-2-s1-p11","mag":"2098423804"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-2-s1-p11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p11","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P11","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/10.1186/1758-2946-2-S1-P11","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057416678","display_name":"Andrea Volkamer","orcid":"https://orcid.org/0000-0002-3760-580X"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I70451448","display_name":"HAW Hamburg","ror":"https://ror.org/00fkqwx76","country_code":"DE","type":"education","lineage":["https://openalex.org/I70451448"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andrea Volkamer","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","Center for Bioinformatics, University of Hamburg Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg Hamburg, Germany","institution_ids":["https://openalex.org/I159176309","https://openalex.org/I70451448"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002611995","display_name":"Thomas Grombacher","orcid":"https://orcid.org/0000-0001-9855-7429"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]},{"id":"https://openalex.org/I862255436","display_name":"Merck Serono S.p.A. (Italy)","ror":"https://ror.org/01z6wpz16","country_code":"IT","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I862255436"]}],"countries":["DE","IT"],"is_corresponding":false,"raw_author_name":"T Grombacher","raw_affiliation_strings":["Bioinformatics, Merck Serono, Frankfurter Str. 250, 64293, Darmstadt, Germany","Bioinformatics, Merck Serono, Darmstadt, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics, Merck Serono, Frankfurter Str. 250, 64293, Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]},{"raw_affiliation_string":"Bioinformatics, Merck Serono, Darmstadt, Germany","institution_ids":["https://openalex.org/I862255436"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I70451448","display_name":"HAW Hamburg","ror":"https://ror.org/00fkqwx76","country_code":"DE","type":"education","lineage":["https://openalex.org/I70451448"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","Center for Bioinformatics, University of Hamburg Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]},{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg Hamburg, Germany","institution_ids":["https://openalex.org/I159176309","https://openalex.org/I70451448"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.3435,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.64178221,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"2","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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":0.9872000217437744,"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/druggability","display_name":"Druggability","score":0.793088436126709},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6566098928451538},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43846818804740906},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38891127705574036},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3543691635131836},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18324065208435059},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13794493675231934}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.793088436126709},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6566098928451538},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43846818804740906},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38891127705574036},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3543691635131836},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18324065208435059},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13794493675231934},{"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":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-2-s1-p11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p11","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P11","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:e0b1cf5e80e64fa99a56527719f7e322","is_oa":false,"landing_page_url":"https://doaj.org/article/e0b1cf5e80e64fa99a56527719f7e322","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 2, Iss Suppl 1, p P11 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2867143","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2867143","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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-2-s1-p11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-2-s1-p11","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-2-S1-P11","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8199999928474426,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098423804.pdf","grobid_xml":"https://content.openalex.org/works/W2098423804.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1979914800","https://openalex.org/W2018408116","https://openalex.org/W2019951137","https://openalex.org/W2031194866","https://openalex.org/W2066143642","https://openalex.org/W2079953901","https://openalex.org/W2092285329","https://openalex.org/W2140407975"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2556855892","https://openalex.org/W4280541024","https://openalex.org/W4214810602","https://openalex.org/W4290613495","https://openalex.org/W3174373983","https://openalex.org/W2099388354","https://openalex.org/W3159447095","https://openalex.org/W2897104689"],"abstract_inverted_index":{"Computer-based":[0],"prediction":[1,81],"of":[2,16,55,68,74,97,100,112,119],"protein":[3,57],"druggability":[4,47,105],"is":[5,65,124],"an":[6],"essential":[7,59],"task":[8],"in":[9,36],"the":[10,52,56,66,69,95,98,101,113,120],"drug":[11,37],"development":[12],"process.":[13],"Early":[14],"identification":[15,67],"disease":[17],"modifying":[18],"targets":[19],"that":[20],"can":[21,28],"be":[22],"modulated":[23],"by":[24],"low-molecular":[25],"weight":[26],"compounds":[27],"help":[29],"to":[30],"speed":[31],"up":[32],"and":[33],"reduce":[34],"costs":[35],"discovery.":[38],"Recently,":[39],"first":[40,60],"methods":[41,64,75,84],"have":[42],"been":[43],"presented":[44],"performing":[45],"a":[46,116],"estimation":[48],"solely":[49],"based":[50,108],"on":[51,94,109],"3D":[53],"structure":[54],"The":[58],"step":[61],"for":[62,77,86,126],"such":[63],"active":[70,79,102,114,121],"site.":[71,103],"A":[72],"multitude":[73],"exist":[76],"automated":[78,87],"site":[80,122],"However,":[82],"most":[83],"developed":[85],"docking":[88],"procedures":[89],"do":[90],"not":[91],"explicitly":[92],"focus":[93],"definition":[96],"boundary":[99],"Since":[104],"estimates":[106],"are":[107],"structural":[110],"descriptors":[111],"site,":[115],"precise":[117],"description":[118],"boundaries":[123],"vital":[125],"correct":[127],"predictions.":[128]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
