{"id":"https://openalex.org/W2299911079","doi":"https://doi.org/10.1186/s12859-016-0983-z","title":"Three-dimensional protein model similarity analysis based on salient shape index","display_name":"Three-dimensional protein model similarity analysis based on salient shape index","publication_year":2016,"publication_date":"2016-03-18","ids":{"openalex":"https://openalex.org/W2299911079","doi":"https://doi.org/10.1186/s12859-016-0983-z","mag":"2299911079","pmid":"https://pubmed.ncbi.nlm.nih.gov/26987968"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-0983-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0983-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0983-z","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/track/pdf/10.1186/s12859-016-0983-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103203554","display_name":"Bo Yao","orcid":"https://orcid.org/0000-0002-4465-4984"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Yao","raw_affiliation_strings":["Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089999424","display_name":"Zhong Li","orcid":"https://orcid.org/0000-0001-9869-006X"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhong Li","raw_affiliation_strings":["Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. lizhong@zstu.edu.cn","Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. lizhong@zstu.edu.cn","institution_ids":["https://openalex.org/I1328775524"]},{"raw_affiliation_string":"Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044585780","display_name":"Meng Ding","orcid":"https://orcid.org/0000-0003-3125-3847"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng Ding","raw_affiliation_strings":["Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033778668","display_name":"Minhong Chen","orcid":"https://orcid.org/0000-0002-3331-3957"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minhong Chen","raw_affiliation_strings":["Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China","institution_ids":["https://openalex.org/I1328775524"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089999424"],"corresponding_institution_ids":["https://openalex.org/I1328775524"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3417,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.67164974,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"17","issue":"1","first_page":"131","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.33250001072883606,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.33250001072883606,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.2578999996185303,"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":0.15160000324249268,"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/index","display_name":"Index (typography)","score":0.6063400506973267},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5576204061508179},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5491046905517578},{"id":"https://openalex.org/keywords/salient","display_name":"Salient","score":0.5141103863716125},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4890754818916321},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4538714289665222},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36549052596092224},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3606865108013153},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35689592361450195},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3247513175010681},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3220381736755371},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25384655594825745},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09680980443954468},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.09177076816558838},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08710503578186035}],"concepts":[{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.6063400506973267},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5576204061508179},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5491046905517578},{"id":"https://openalex.org/C2780719617","wikidata":"https://www.wikidata.org/wiki/Q1030752","display_name":"Salient","level":2,"score":0.5141103863716125},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4890754818916321},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4538714289665222},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36549052596092224},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3606865108013153},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35689592361450195},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3247513175010681},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3220381736755371},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25384655594825745},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09680980443954468},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09177076816558838},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08710503578186035},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"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":"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":"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":"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":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-016-0983-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0983-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0983-z","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:26987968","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26987968","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:pubmedcentral.nih.gov:4797110","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4797110","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/s12859-016-0983-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-0983-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-0983-z","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":[{"id":"https://openalex.org/G3072570188","display_name":null,"funder_award_id":"LY14A010032","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"},{"id":"https://openalex.org/G7516577642","display_name":null,"funder_award_id":"51075421","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321106","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934"},{"id":"https://openalex.org/F4320324847","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55"},{"id":"https://openalex.org/F4320332427","display_name":"School of Medicine, Stanford University","ror":"https://ror.org/00f54p054"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2299911079.pdf","grobid_xml":"https://content.openalex.org/works/W2299911079.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W64245849","https://openalex.org/W2007206727","https://openalex.org/W2010209818","https://openalex.org/W2038310524","https://openalex.org/W2053008628","https://openalex.org/W2053939793","https://openalex.org/W2057251215","https://openalex.org/W2066029809","https://openalex.org/W2066880292","https://openalex.org/W2070058191","https://openalex.org/W2077976550","https://openalex.org/W2100900426","https://openalex.org/W2112946416","https://openalex.org/W2113149602","https://openalex.org/W2114795971","https://openalex.org/W2133245851","https://openalex.org/W2134601920","https://openalex.org/W2148219066","https://openalex.org/W2149708440","https://openalex.org/W2151554142","https://openalex.org/W2153850637","https://openalex.org/W2161160262","https://openalex.org/W2165939338","https://openalex.org/W2308071406","https://openalex.org/W4230357944","https://openalex.org/W4285719527","https://openalex.org/W6675545231","https://openalex.org/W6680120578"],"related_works":["https://openalex.org/W2329500892","https://openalex.org/W28991112","https://openalex.org/W2370726991","https://openalex.org/W2369710579","https://openalex.org/W2545348020","https://openalex.org/W4327728159","https://openalex.org/W2912751582","https://openalex.org/W2130893381","https://openalex.org/W1990856605","https://openalex.org/W3120436346"],"abstract_inverted_index":{"BACKGROUND:":[0],"Proteins":[1],"play":[2],"a":[3,12,23,65,80],"special":[4],"role":[5],"in":[6],"bioinformatics.":[7],"The":[8,35],"surface":[9],"shape":[10,92],"of":[11,19,46,59],"protein,":[13,21],"which":[14,50],"is":[15,76,151],"an":[16,43],"important":[17,44],"characteristic":[18],"the":[20,29,54,57,91,96,105,115,126,133,138,157],"defines":[22],"geometric":[24,99],"and":[25,56,95,102,114,137,153],"biochemical":[26],"domain":[27],"where":[28],"protein":[30,39,47,67,74,86,106,147],"interacts":[31],"with":[32],"other":[33],"proteins.":[34,60],"similarity":[36,68,108,148],"analysis":[37,69,149],"among":[38],"models":[40,75],"has":[41],"become":[42],"topic":[45],"analysis,":[48],"by":[49,89,109],"it":[51],"can":[52],"reveal":[53],"structure":[55],"function":[58],"RESULTS:":[61],"In":[62],"this":[63,111],"paper,":[64],"new":[66],"method":[70,124,136,150],"based":[71],"on":[72],"three-dimensional":[73],"proposed.":[77],"It":[78],"constructs":[79],"feature":[81,100,112],"matrix":[82,113],"descriptor":[83,140],"for":[84],"each":[85],"model":[87,107],"combined":[88],"calculating":[90],"index":[93],"(SI)":[94],"related":[97],"salient":[98],"(SGF),":[101],"then":[103],"analyzes":[104],"using":[110],"extended":[116],"grey":[117],"relation":[118],"analysis.":[119],"CONCLUSIONS:":[120],"We":[121],"compare":[122],"our":[123,146],"to":[125],"Multi-resolution":[127],"Reeb":[128],"Graph":[129],"(MRG)":[130],"skeleton":[131,135],"method,":[132],"L1-medial":[134],"local-diameter":[139],"method.":[141],"Experimental":[142],"results":[143],"show":[144],"that":[145],"accurate":[152],"reliable":[154],"while":[155],"keeping":[156],"high":[158],"computational":[159],"efficiency.":[160]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
