{"id":"https://openalex.org/W2069088045","doi":"https://doi.org/10.1142/s021972000700276x","title":"CAVITY SCALING: AUTOMATED REFINEMENT OF CAVITY-AWARE MOTIFS IN PROTEIN FUNCTION PREDICTION","display_name":"CAVITY SCALING: AUTOMATED REFINEMENT OF CAVITY-AWARE MOTIFS IN PROTEIN FUNCTION PREDICTION","publication_year":2007,"publication_date":"2007-04-01","ids":{"openalex":"https://openalex.org/W2069088045","doi":"https://doi.org/10.1142/s021972000700276x","mag":"2069088045","pmid":"https://pubmed.ncbi.nlm.nih.gov/17589966"},"language":"en","primary_location":{"id":"doi:10.1142/s021972000700276x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000700276x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5062182398","display_name":"Brian Y. Chen","orcid":"https://orcid.org/0000-0001-9025-0107"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"BRIAN Y. CHEN","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX 77005, USA","Department of Computer Science, Rice University, Houston TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087145328","display_name":"Drew Bryant","orcid":"https://orcid.org/0000-0001-7781-7033"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DREW H. BRYANT","raw_affiliation_strings":["Department of Bioengineering, Rice University, Houston, TX 77005, USA","Department of Bioengineering, Rice University, Houston, TX 77005,#N#USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Bioengineering, Rice University, Houston, TX 77005,#N#USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035723276","display_name":"Viacheslav Y. Fofanov","orcid":"https://orcid.org/0000-0001-7142-0764"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"VIACHESLAV Y. FOFANOV","raw_affiliation_strings":["Department of Statistics, Rice University, Houston, TX 77005, USA","Department of Statistics, Rice University, Houston, TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042113315","display_name":"David M. Kristensen","orcid":"https://orcid.org/0000-0003-0657-1632"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DAVID M. KRISTENSEN","raw_affiliation_strings":["Program in Structural Computational, Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Structural Computational, Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042406781","display_name":"Amanda E. Cruess","orcid":null},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"AMANDA E. CRUESS","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, TX 77005, USA","Department of Computer Science, Rice University, Houston TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071222148","display_name":"Marek Kimmel","orcid":"https://orcid.org/0000-0001-8161-890X"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"MAREK KIMMEL","raw_affiliation_strings":["Department of Statistics, Rice University, Houston, TX 77005, USA","Department of Statistics, Rice University, Houston, TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023680746","display_name":"Olivier Lichtarge","orcid":"https://orcid.org/0000-0003-4057-7122"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"OLIVIER LICHTARGE","raw_affiliation_strings":["Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA","Program in Structural Computational, Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Program in Structural Computational, Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"LYDIA E. KAVRAKI","raw_affiliation_strings":["Department of Bioengineering, Rice University, Houston, TX 77005, USA","Department of Computer Science, Rice University, Houston, TX 77005, USA","Program in Structural Computational, Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, TX 77005, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Program in Structural Computational, Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7994,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.71010613,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"05","issue":"02a","first_page":"353","last_page":"382"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9980999827384949,"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"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9904999732971191,"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/false-positive-paradox","display_name":"False positive paradox","score":0.7993217706680298},{"id":"https://openalex.org/keywords/substructure","display_name":"Substructure","score":0.7881764769554138},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.6377997994422913},{"id":"https://openalex.org/keywords/spheres","display_name":"SPHERES","score":0.53615802526474},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.534675657749176},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5013027191162109},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.4820183515548706},{"id":"https://openalex.org/keywords/true-positive-rate","display_name":"True positive rate","score":0.46232086420059204},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4395488202571869},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38389456272125244},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3228234052658081},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31285202503204346},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1952207088470459},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.1875496506690979},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1363523304462433}],"concepts":[{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7993217706680298},{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.7881764769554138},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.6377997994422913},{"id":"https://openalex.org/C72422203","wikidata":"https://www.wikidata.org/wiki/Q7392545","display_name":"SPHERES","level":2,"score":0.53615802526474},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.534675657749176},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5013027191162109},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.4820183515548706},{"id":"https://openalex.org/C2989486834","wikidata":"https://www.wikidata.org/wiki/Q3808900","display_name":"True positive rate","level":2,"score":0.46232086420059204},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4395488202571869},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38389456272125244},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3228234052658081},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31285202503204346},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1952207088470459},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.1875496506690979},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1363523304462433},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s021972000700276x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000700276x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:17589966","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17589966","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":80,"referenced_works":["https://openalex.org/W56333015","https://openalex.org/W187096958","https://openalex.org/W1519996426","https://openalex.org/W1570722626","https://openalex.org/W1585634379","https://openalex.org/W1950941644","https://openalex.org/W1954690293","https://openalex.org/W1963538288","https://openalex.org/W1969125290","https://openalex.org/W1972159725","https://openalex.org/W1974638435","https://openalex.org/W1975563330","https://openalex.org/W1978462051","https://openalex.org/W1981095470","https://openalex.org/W1983036219","https://openalex.org/W1984563996","https://openalex.org/W1992115216","https://openalex.org/W1992558926","https://openalex.org/W1993684667","https://openalex.org/W1995945562","https://openalex.org/W1999319994","https://openalex.org/W2000794695","https://openalex.org/W2001289883","https://openalex.org/W2013557222","https://openalex.org/W2025967846","https://openalex.org/W2029641302","https://openalex.org/W2030650909","https://openalex.org/W2033339543","https://openalex.org/W2035391529","https://openalex.org/W2040407936","https://openalex.org/W2042647264","https://openalex.org/W2044772240","https://openalex.org/W2045639174","https://openalex.org/W2047306549","https://openalex.org/W2051895548","https://openalex.org/W2052232788","https://openalex.org/W2055448320","https://openalex.org/W2058463742","https://openalex.org/W2067455153","https://openalex.org/W2076744915","https://openalex.org/W2078290150","https://openalex.org/W2084482738","https://openalex.org/W2085277871","https://openalex.org/W2086995578","https://openalex.org/W2088534163","https://openalex.org/W2091563009","https://openalex.org/W2101532349","https://openalex.org/W2102333330","https://openalex.org/W2104245738","https://openalex.org/W2105902442","https://openalex.org/W2107327414","https://openalex.org/W2108067237","https://openalex.org/W2108508060","https://openalex.org/W2110401277","https://openalex.org/W2112688502","https://openalex.org/W2115451817","https://openalex.org/W2117164735","https://openalex.org/W2126728600","https://openalex.org/W2133990057","https://openalex.org/W2135338271","https://openalex.org/W2136567909","https://openalex.org/W2137991504","https://openalex.org/W2139942857","https://openalex.org/W2140407975","https://openalex.org/W2141451123","https://openalex.org/W2144071905","https://openalex.org/W2146939455","https://openalex.org/W2146940292","https://openalex.org/W2149432763","https://openalex.org/W2150445050","https://openalex.org/W2152358306","https://openalex.org/W2153504150","https://openalex.org/W2154204736","https://openalex.org/W2159400443","https://openalex.org/W2160085559","https://openalex.org/W2162574056","https://openalex.org/W2228774462","https://openalex.org/W2328218756","https://openalex.org/W3106889297","https://openalex.org/W3167825259"],"related_works":["https://openalex.org/W2027184711","https://openalex.org/W3129715955","https://openalex.org/W1557094818","https://openalex.org/W4287692494","https://openalex.org/W3047594718","https://openalex.org/W4299651861","https://openalex.org/W2953243682","https://openalex.org/W3027053746","https://openalex.org/W4386222044","https://openalex.org/W2099261052"],"abstract_inverted_index":{"Algorithms":[0],"for":[1,12],"geometric":[2,26,163],"and":[3,27,35,71,100,164,188],"chemical":[4,28,165],"comparison":[5,166],"of":[6,25,37,45,50,60,74,134,179,186,199],"protein":[7,16],"substructure":[8],"can":[9,54,136,157,181],"be":[10,55,137,158],"useful":[11],"many":[13],"applications":[14],"in":[15],"function":[17,46],"prediction.":[18],"These":[19],"motif":[20,51,93,120],"matching":[21,52],"algorithms":[22,53],"identify":[23],"matches":[24,63,77,117],"similarity":[29],"between":[30],"well-studied":[31],"functional":[32],"sites,":[33],"motifs,":[34],"substructures":[36],"functionally":[38,65,79,97,104],"uncharacterized":[39],"proteins,":[40,67,81],"targets.":[41],"For":[42],"the":[43,48,58,72,132,177,184,196],"purpose":[44],"prediction,":[47],"accuracy":[49,169],"evaluated":[56],"with":[57,140],"number":[59,73,185],"statistically":[61,75],"significant":[62,98,105],"to":[64,78,95,102,131,160,212],"related":[66],"true":[68],"positives":[69,83],"(TPs),":[70],"insignificant":[76],"unrelated":[80],"false":[82],"(FPs).":[84],"Our":[85],"earlier":[86,151],"work":[87,152],"developed":[88],"cavity-aware":[89,110,193],"motifs":[90,111],"which":[91,128],"use":[92],"points":[94],"represent":[96,103],"atoms":[99],"C-spheres":[101,156,180,200],"volumes.":[106],"We":[107,122,173],"observed":[108,124],"that":[109,125,155,176],"match":[112],"significantly":[113,129,182],"fewer":[114],"FPs":[115,189],"than":[116],"containing":[118],"only":[119],"points.":[121],"also":[123,174],"high-impact":[126],"C-spheres,":[127],"contribute":[130],"reduction":[133],"FPs,":[135],"isolated":[138],"automatically":[139],"a":[141,192,202],"technique":[142],"we":[143,206],"call":[144],"Cavity":[145],"Scaling.":[146],"This":[147],"paper":[148],"extends":[149],"our":[150],"by":[153,191],"demonstrating":[154],"used":[159],"accelerate":[161],"point-based":[162],"algorithms,":[167],"maintaining":[168],"while":[170],"reducing":[171],"runtime.":[172],"demonstrate":[175],"placement":[178,198,210],"affect":[183],"TPs":[187],"identified":[190],"motif.":[194],"While":[195],"optimal":[197],"remains":[201],"difficult":[203],"open":[204],"problem,":[205],"compared":[207],"two":[208],"logical":[209],"strategies":[211],"better":[213],"understand":[214],"C-sphere":[215],"placement.":[216]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}