{"id":"https://openalex.org/W2155072429","doi":"https://doi.org/10.1186/1471-2105-7-40","title":"Protein structure similarity from principle component correlation analysis","display_name":"Protein structure similarity from principle component correlation analysis","publication_year":2006,"publication_date":"2006-01-25","ids":{"openalex":"https://openalex.org/W2155072429","doi":"https://doi.org/10.1186/1471-2105-7-40","mag":"2155072429","pmid":"https://pubmed.ncbi.nlm.nih.gov/16436213"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-40","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-40","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-40","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-40","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053033228","display_name":"Xiaobo Zhou","orcid":"https://orcid.org/0000-0002-7127-2869"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaobo Zhou","raw_affiliation_strings":["Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, Boston, MA 02215, USA. zhou@crystal.harvard.edu","Harvard Center for Neurodegeneration and Repair \u2013 Center for Bioinformatics, Harvard Medical School, 1249 Boylston Street, Boston, MA, 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, Boston, MA 02215, USA. zhou@crystal.harvard.edu","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Harvard Center for Neurodegeneration and Repair \u2013 Center for Bioinformatics, Harvard Medical School, 1249 Boylston Street, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030377405","display_name":"James J. Chou","orcid":"https://orcid.org/0000-0002-4442-0344"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Chou","raw_affiliation_strings":["Department of Biological Chemistry and Molecular Pharmacology, Harvard Medial School, 240 Longwood Avenue, Boston, MA, 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry and Molecular Pharmacology, Harvard Medial School, 240 Longwood Avenue, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015077092","display_name":"Stephen T.C. Wong","orcid":"https://orcid.org/0000-0001-9188-6502"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210166946","display_name":"Imaging Center","ror":"https://ror.org/05hsqsk33","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210166946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen TC Wong","raw_affiliation_strings":["Functional and Molecular Imaging Center, Radiology Department, Brigham and Women's Hospital, One Brigham Circle, 1620 Tremont Street, Boston, MA, 02121, USA","Harvard Center for Neurodegeneration and Repair \u2013 Center for Bioinformatics, Harvard Medical School, 1249 Boylston Street, Boston, MA, 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional and Molecular Imaging Center, Radiology Department, Brigham and Women's Hospital, One Brigham Circle, 1620 Tremont Street, Boston, MA, 02121, USA","institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I4210166946"]},{"raw_affiliation_string":"Harvard Center for Neurodegeneration and Repair \u2013 Center for Bioinformatics, Harvard Medical School, 1249 Boylston Street, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5455,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.65949554,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"7","issue":"1","first_page":"40","last_page":"40"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6891999840736389,"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":0.6891999840736389,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.07720000296831131,"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":0.07460000365972519,"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/similarity","display_name":"Similarity (geometry)","score":0.6614892482757568},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.6222925186157227},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.5443482398986816},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5289039015769958},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5247081518173218},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.49595174193382263},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.4940243363380432},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.47765958309173584},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.4472077786922455},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.44220221042633057},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4128863513469696},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.39603328704833984},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.385002464056015},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3826502561569214},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.36206626892089844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34782999753952026},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.27304649353027344},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.24521684646606445},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.24325111508369446},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2217406928539276},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21099266409873962},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.158664733171463},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14838477969169617},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.12403696775436401},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1202704906463623},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08641013503074646}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6614892482757568},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.6222925186157227},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.5443482398986816},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5289039015769958},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5247081518173218},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.49595174193382263},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.4940243363380432},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.47765958309173584},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.4472077786922455},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.44220221042633057},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4128863513469696},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.39603328704833984},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.385002464056015},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3826502561569214},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36206626892089844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34782999753952026},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27304649353027344},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.24521684646606445},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.24325111508369446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2217406928539276},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21099266409873962},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.158664733171463},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14838477969169617},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.12403696775436401},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1202704906463623},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08641013503074646},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"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/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","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":"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":"D003461","descriptor_name":"Crystallography","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003461","descriptor_name":"Crystallography","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003461","descriptor_name":"Crystallography","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"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":"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":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-7-40","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-40","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-40","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16436213","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16436213","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:11c56a8050714d0d9a42a2abe78fd8e6","is_oa":false,"landing_page_url":"https://doaj.org/article/11c56a8050714d0d9a42a2abe78fd8e6","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":"BMC Bioinformatics, Vol 7, Iss 1, p 40 (2006)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1386710","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1386710","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-40","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-40","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-40","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155072429.pdf","grobid_xml":"https://content.openalex.org/works/W2155072429.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1542067597","https://openalex.org/W1588131283","https://openalex.org/W1966521833","https://openalex.org/W1967501922","https://openalex.org/W1979389134","https://openalex.org/W1987713050","https://openalex.org/W1992577925","https://openalex.org/W2006211612","https://openalex.org/W2007828112","https://openalex.org/W2015692100","https://openalex.org/W2039533030","https://openalex.org/W2041938888","https://openalex.org/W2085972085","https://openalex.org/W2108067237","https://openalex.org/W2110483430","https://openalex.org/W2116587369","https://openalex.org/W2126016150","https://openalex.org/W2130479394","https://openalex.org/W2148376194","https://openalex.org/W2151785844","https://openalex.org/W2152221363","https://openalex.org/W2158275234","https://openalex.org/W2158815406","https://openalex.org/W2167197805","https://openalex.org/W2167656653","https://openalex.org/W2595753002","https://openalex.org/W4298348465"],"related_works":["https://openalex.org/W2075451741","https://openalex.org/W2169682455","https://openalex.org/W2070693796","https://openalex.org/W2044467472","https://openalex.org/W2154685897","https://openalex.org/W2014499409","https://openalex.org/W2821108685","https://openalex.org/W4232453105","https://openalex.org/W2009804911","https://openalex.org/W2062222431"],"abstract_inverted_index":{"BACKGROUND:":[0],"Owing":[1],"to":[2,77,105,114,191,224],"rapid":[3],"expansion":[4],"of":[5,13,29,38,64,98,134,170,188,203,206,262,283],"protein":[6,108,155,220,295],"structure":[7,14,137,156,296],"databases":[8],"in":[9,22,34,54,84,112,183,270,289],"recent":[10],"years,":[11],"methods":[12],"comparison":[15,261],"are":[16,71,196,230],"becoming":[17],"increasingly":[18],"effective":[19,269],"and":[20,31,118],"important":[21],"revealing":[23],"novel":[24],"information":[25],"on":[26],"functional":[27],"properties":[28],"proteins":[30,47,85,99,128,242],"their":[32,55,135,263],"roles":[33],"the":[35,42,51,61,69,79,131,143,168,184,200,225,280],"grand":[36],"scheme":[37],"evolutionary":[39],"biology.":[40],"Currently,":[41],"structural":[43,66,120,125,176,292],"similarity":[44,67,126],"between":[45,127,162,199],"two":[46,256],"is":[48,60,157,216,286],"measured":[49],"by":[50,129,233],"root-mean-square-deviation":[52],"(RMSD)":[53],"best-superimposed":[56],"atomic":[57],"coordinates.":[58],"RMSD":[59,234],"golden":[62],"rule":[63],"measuring":[65],"when":[68,254],"structures":[70,109,221],"nearly":[72],"identical;":[73],"it,":[74],"however,":[75],"fails":[76],"detect":[78],"higher":[80],"order":[81,113],"topological":[82,227,248],"similarities":[83],"evolved":[86],"into":[87],"different":[88,232,247],"shapes.":[89],"We":[90,123,277],"propose":[91],"new":[92],"algorithms":[93],"for":[94,153,219,294],"extracting":[95],"geometrical":[96],"invariants":[97],"that":[100,165,222,253,279],"can":[101,166,239,266],"be":[102,267],"effectively":[103],"used":[104],"identify":[106],"homologous":[107],"or":[110,173,186,208,273],"topologies":[111],"quantify":[115],"both":[116],"close":[117],"remote":[119],"similarities.":[121],"RESULTS:":[122],"measure":[124],"correlating":[130],"principle":[132,201],"components":[133,202],"secondary":[136,163],"interaction":[138,151,204,259,284],"matrix.":[139],"In":[140],"our":[141],"approach,":[142],"Principle":[144],"Component":[145],"Correlation":[146],"(PCC)":[147],"analysis,":[148],"a":[149,154,180],"symmetric":[150],"matrix":[152,285],"constructed":[158],"with":[159],"relationship":[160],"parameters":[161,293],"elements":[164],"take":[167],"form":[169],"distance,":[171],"orientation,":[172],"other":[174],"relevant":[175],"invariants.":[177],"When":[178],"using":[179,255],"distance-based":[181],"construction":[182],"presence":[185],"absence":[187],"encoded":[189],"N":[190],"C":[192],"terminal":[193],"sense,":[194],"there":[195],"strong":[197],"correlations":[198],"matrices":[205],"structurally":[207,272],"topologically":[209,274],"similar":[210,244,275],"proteins.":[211,276],"CONCLUSION:":[212],"The":[213,236],"PCC":[214,237,281],"method":[215],"extensively":[217],"tested":[218],"belong":[223],"same":[226],"class":[228],"but":[229,246],"significantly":[231],"measure.":[235],"analysis":[238,282],"also":[240],"differentiate":[241],"having":[243],"shapes":[245],"arrangements.":[249],"Additionally,":[250],"we":[251],"demonstrate":[252],"independently":[257],"defined":[258],"matrices,":[260],"maximum":[264],"eigenvalues":[265],"highly":[268,287],"clustering":[271],"believe":[278],"flexible":[288],"adopting":[290],"various":[291],"comparison.":[297]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
