{"id":"https://openalex.org/W2002278080","doi":"https://doi.org/10.1021/ci5005898","title":"Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real","display_name":"Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real","publication_year":2014,"publication_date":"2014-12-05","ids":{"openalex":"https://openalex.org/W2002278080","doi":"https://doi.org/10.1021/ci5005898","mag":"2002278080","pmid":"https://pubmed.ncbi.nlm.nih.gov/25474400"},"language":"en","primary_location":{"id":"doi:10.1021/ci5005898","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5005898","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/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":false,"raw_author_name":"Timo Krotzky","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006998913","display_name":"Christian Grunwald","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164510","display_name":"BioCrea (Germany)","ror":"https://ror.org/05rxdtg07","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210164510"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Grunwald","raw_affiliation_strings":["BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany","BioCrea GmbH, Meissner Strasse#R#191, 01445 Radebeul, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany","institution_ids":["https://openalex.org/I4210164510"]},{"raw_affiliation_string":"BioCrea GmbH, Meissner Strasse#R#191, 01445 Radebeul, Germany","institution_ids":["https://openalex.org/I4210164510"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046071135","display_name":"Ute Egerland","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164510","display_name":"BioCrea (Germany)","ror":"https://ror.org/05rxdtg07","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210164510"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ute Egerland","raw_affiliation_strings":["BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany","BioCrea GmbH, Meissner Strasse#R#191, 01445 Radebeul, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany","institution_ids":["https://openalex.org/I4210164510"]},{"raw_affiliation_string":"BioCrea GmbH, Meissner Strasse#R#191, 01445 Radebeul, Germany","institution_ids":["https://openalex.org/I4210164510"]}]},{"author_position":"last","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":true,"raw_author_name":"Gerhard Klebe","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005420915"],"corresponding_institution_ids":["https://openalex.org/I161103922"],"apc_list":null,"apc_paid":null,"fwci":1.7868,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.8454302,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"55","issue":"1","first_page":"165","last_page":"179"},"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":0.9850999712944031,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9775000214576721,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6318942308425903},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.6221197247505188},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5681607723236084},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.47446781396865845},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.44832366704940796},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.42363500595092773},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3646312952041626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33495327830314636},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28881821036338806},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19934862852096558},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15165382623672485},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14860230684280396}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6318942308425903},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6221197247505188},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5681607723236084},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.47446781396865845},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.44832366704940796},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.42363500595092773},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3646312952041626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33495327830314636},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28881821036338806},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19934862852096558},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15165382623672485},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14860230684280396},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":[{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009243","descriptor_name":"NAD","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009243","descriptor_name":"NAD","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009243","descriptor_name":"NAD","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","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":"D016194","descriptor_name":"Receptors, N-Methyl-D-Aspartate","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D016194","descriptor_name":"Receptors, N-Methyl-D-Aspartate","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D016194","descriptor_name":"Receptors, N-Methyl-D-Aspartate","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D016194","descriptor_name":"Receptors, N-Methyl-D-Aspartate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016194","descriptor_name":"Receptors, N-Methyl-D-Aspartate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016194","descriptor_name":"Receptors, N-Methyl-D-Aspartate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":2,"locations":[{"id":"doi:10.1021/ci5005898","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5005898","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:25474400","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25474400","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7200000286102295}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":79,"referenced_works":["https://openalex.org/W127144385","https://openalex.org/W567117013","https://openalex.org/W1963538288","https://openalex.org/W1965161138","https://openalex.org/W1965555277","https://openalex.org/W1974638435","https://openalex.org/W1974971448","https://openalex.org/W1978787457","https://openalex.org/W1979132333","https://openalex.org/W1979414133","https://openalex.org/W1981064967","https://openalex.org/W1984591534","https://openalex.org/W1986154009","https://openalex.org/W1992578437","https://openalex.org/W1998568556","https://openalex.org/W1999623718","https://openalex.org/W2000077914","https://openalex.org/W2000482836","https://openalex.org/W2003165115","https://openalex.org/W2003356525","https://openalex.org/W2003610577","https://openalex.org/W2009393104","https://openalex.org/W2017100743","https://openalex.org/W2021953523","https://openalex.org/W2021954541","https://openalex.org/W2023119578","https://openalex.org/W2024463335","https://openalex.org/W2030650909","https://openalex.org/W2030686695","https://openalex.org/W2031194866","https://openalex.org/W2040595595","https://openalex.org/W2043583897","https://openalex.org/W2045656688","https://openalex.org/W2055043387","https://openalex.org/W2057350662","https://openalex.org/W2062352340","https://openalex.org/W2066199490","https://openalex.org/W2076274126","https://openalex.org/W2077529366","https://openalex.org/W2081201773","https://openalex.org/W2085176241","https://openalex.org/W2085277871","https://openalex.org/W2086380285","https://openalex.org/W2089085945","https://openalex.org/W2089094370","https://openalex.org/W2091708007","https://openalex.org/W2097311600","https://openalex.org/W2101220662","https://openalex.org/W2101223914","https://openalex.org/W2101973479","https://openalex.org/W2102333330","https://openalex.org/W2102997946","https://openalex.org/W2108067237","https://openalex.org/W2110401277","https://openalex.org/W2116007667","https://openalex.org/W2118190420","https://openalex.org/W2119470100","https://openalex.org/W2120138074","https://openalex.org/W2122365200","https://openalex.org/W2124134368","https://openalex.org/W2124850224","https://openalex.org/W2130479394","https://openalex.org/W2131260462","https://openalex.org/W2131285288","https://openalex.org/W2137345862","https://openalex.org/W2139362074","https://openalex.org/W2139976683","https://openalex.org/W2140058398","https://openalex.org/W2142721960","https://openalex.org/W2146940292","https://openalex.org/W2153153865","https://openalex.org/W2155653793","https://openalex.org/W2157825442","https://openalex.org/W2162454135","https://openalex.org/W2165925807","https://openalex.org/W2208175234","https://openalex.org/W2292572876","https://openalex.org/W2295332248","https://openalex.org/W2745750801"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W4389116644","https://openalex.org/W3129816939","https://openalex.org/W2153315159","https://openalex.org/W3174709249","https://openalex.org/W2017055503","https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2594726310","https://openalex.org/W2355193834"],"abstract_inverted_index":{"Determination":[0],"of":[1,33,54,68,101,136,151,213,219,237,240],"structural":[2],"similarities":[3],"between":[4],"protein":[5,56],"binding":[6,57,62,82,130],"pockets":[7],"is":[8,222],"an":[9],"important":[10],"challenge":[11],"in":[12,13,205],"silico":[14],"drug":[15],"design.":[16],"It":[17],"can":[18,76],"help":[19],"to":[20,35,79,89,97],"understand":[21],"selectivity":[22],"considerations,":[23],"predict":[24],"unexpected":[25],"ligand":[26],"cross-reactivity,":[27],"and":[28,52,75,94,143,164,176,184],"support":[29],"the":[30,48,102,173,177,193,235,241],"putative":[31,55],"annotation":[32],"function":[34],"orphan":[36],"proteins.":[37],"To":[38],"this":[39,60,106],"end,":[40],"Cavbase":[41,121,199],"was":[42],"developed":[43,204],"as":[44,66],"a":[45,116,149,211,226],"tool":[46],"for":[47,120,125,234],"automated":[49],"detection,":[50],"storage,":[51],"classification":[53,183],"sites.":[58],"In":[59,105],"context,":[61],"sites":[63,131],"are":[64,132,140],"characterized":[65],"sets":[67,135,163],"pseudocenters,":[69],"which":[70],"denote":[71],"surface-exposed":[72],"physicochemical":[73],"properties,":[74],"be":[77,90],"used":[78],"enable":[80],"mutual":[81],"site":[83],"comparisons.":[84,128],"However,":[85],"these":[86],"comparisons":[87,156],"tend":[88],"computationally":[91],"very":[92,98],"demanding":[93],"often":[95],"lead":[96],"slow":[99],"computations":[100],"similarity":[103,127],"measures.":[104],"study,":[107],"we":[108],"propose":[109],"RAPMAD":[110,187],"(RApid":[111],"Pocket":[112],"MAtching":[113],"using":[114],"Distances),":[115],"new":[117],"evaluation":[118],"formalism":[119,195],"entries":[122],"that":[123,139,232],"allows":[124],"ultrafast":[126],"Protein":[129],"represented":[133],"by":[134,180,225],"distance":[137],"histograms":[138],"both":[141],"generated":[142],"compared":[144],"with":[145],"linear":[146],"complexity.":[147],"Attaining":[148],"speed":[150],"more":[152],"than":[153,192],"20":[154],"000":[155],"per":[157],"second,":[158],"screenings":[159],"across":[160],"large":[161],"data":[162],"even":[165],"entire":[166],"databases":[167],"become":[168],"easily":[169],"feasible.":[170],"We":[171],"demonstrate":[172],"discriminative":[174],"power":[175],"short":[178],"runtime":[179],"performing":[181],"several":[182,201],"retrieval":[185],"experiments.":[186],"attains":[188],"better":[189],"success":[190],"rates":[191],"comparison":[194],"originally":[196],"implemented":[197],"into":[198],"or":[200],"alternative":[202],"approaches":[203],"recent":[206],"time,":[207],"while":[208],"requiring":[209],"only":[210],"fraction":[212],"their":[214],"runtime.":[215],"The":[216],"pratical":[217],"use":[218],"our":[220],"method":[221],"finally":[223],"proven":[224],"successful":[227],"prospective":[228],"virtual":[229],"screening":[230],"study":[231],"aims":[233],"identification":[236],"novel":[238],"inhibitors":[239],"NMDA":[242],"receptor.":[243]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}