{"id":"https://openalex.org/W3101574558","doi":"https://doi.org/10.1186/s13040-016-0108-2","title":"ProtNN: fast and accurate protein 3D-structure classification in structural and topological space","display_name":"ProtNN: fast and accurate protein 3D-structure classification in structural and topological space","publication_year":2016,"publication_date":"2016-09-23","ids":{"openalex":"https://openalex.org/W3101574558","doi":"https://doi.org/10.1186/s13040-016-0108-2","mag":"3101574558","pmid":"https://pubmed.ncbi.nlm.nih.gov/27688811"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-016-0108-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0108-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-016-0108-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-016-0108-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072789724","display_name":"Wajdi Dhifli","orcid":"https://orcid.org/0000-0002-6580-8778"},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Wajdi Dhifli","raw_affiliation_strings":["Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8 Canada","Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8 Canada","institution_ids":["https://openalex.org/I159129438"]},{"raw_affiliation_string":"Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8, Canada","institution_ids":["https://openalex.org/I159129438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061553529","display_name":"Abdoulaye Banir\u00e9 Diallo","orcid":"https://orcid.org/0000-0002-1168-9371"},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Abdoulaye Banir\u00e9 Diallo","raw_affiliation_strings":["Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8 Canada","Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8, Canada"],"raw_orcid":"https://orcid.org/0000-0002-1168-9371","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8 Canada","institution_ids":["https://openalex.org/I159129438"]},{"raw_affiliation_string":"Department of Computer Science, University of Quebec At Montreal, PO box 8888, Downtown stationMontreal, H3C 3P8, Canada","institution_ids":["https://openalex.org/I159129438"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5061553529"],"corresponding_institution_ids":["https://openalex.org/I159129438"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":0.9621,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.77719309,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"9","issue":"1","first_page":"30","last_page":"30"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.784500002861023,"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":0.784500002861023,"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":0.0568000003695488,"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":0.056299999356269836,"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/computer-science","display_name":"Computer science","score":0.6535835266113281},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5711544752120972},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4807950556278229},{"id":"https://openalex.org/keywords/topological-space","display_name":"Topological space","score":0.41795897483825684},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3873053193092346},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33153533935546875},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3115929365158081},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1638222336769104},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.10701984167098999},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08302149176597595}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6535835266113281},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5711544752120972},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4807950556278229},{"id":"https://openalex.org/C81332173","wikidata":"https://www.wikidata.org/wiki/Q179899","display_name":"Topological space","level":2,"score":0.41795897483825684},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3873053193092346},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33153533935546875},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3115929365158081},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1638222336769104},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.10701984167098999},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08302149176597595},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-016-0108-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0108-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-016-0108-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:27688811","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27688811","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":"BioData mining","raw_type":null},{"id":"pmh:oai:arXiv.org:1511.00736","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1511.00736","pdf_url":"https://arxiv.org/pdf/1511.00736","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5034655","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5034655","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":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-016-0108-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0108-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-016-0108-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3101574558.pdf","grobid_xml":"https://content.openalex.org/works/W3101574558.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W85648037","https://openalex.org/W1235360365","https://openalex.org/W1499824784","https://openalex.org/W1516019649","https://openalex.org/W1543932334","https://openalex.org/W1970371025","https://openalex.org/W1974099839","https://openalex.org/W1979871945","https://openalex.org/W1984794455","https://openalex.org/W1998490996","https://openalex.org/W1998931880","https://openalex.org/W2048947602","https://openalex.org/W2055043387","https://openalex.org/W2094826395","https://openalex.org/W2097642323","https://openalex.org/W2099179622","https://openalex.org/W2099438806","https://openalex.org/W2100161738","https://openalex.org/W2101940264","https://openalex.org/W2102039273","https://openalex.org/W2110920461","https://openalex.org/W2111708605","https://openalex.org/W2112090702","https://openalex.org/W2114062029","https://openalex.org/W2115848690","https://openalex.org/W2119821739","https://openalex.org/W2128653811","https://openalex.org/W2130479394","https://openalex.org/W2134789671","https://openalex.org/W2143426320","https://openalex.org/W2145388307","https://openalex.org/W2148830285","https://openalex.org/W2151554678","https://openalex.org/W2152326664","https://openalex.org/W2157242929","https://openalex.org/W2157965775","https://openalex.org/W2160672469","https://openalex.org/W2164281374","https://openalex.org/W2769133055","https://openalex.org/W4298468057","https://openalex.org/W6684335045"],"related_works":["https://openalex.org/W4309710663","https://openalex.org/W2116865742","https://openalex.org/W2081579710","https://openalex.org/W2371641196","https://openalex.org/W2000850197","https://openalex.org/W2367065563","https://openalex.org/W2038905316","https://openalex.org/W1921169094","https://openalex.org/W366410996","https://openalex.org/W2980021896"],"abstract_inverted_index":{"BACKGROUND:":[0],"Studying":[1],"the":[2,12,30,50,59,90,93,96,102,117,136,139],"functions":[3],"and":[4,40,55,81,129,138,145],"structures":[5,23,57,121,142],"of":[6,15,19,32,53,61,84,99,116,135,199,202],"proteins":[7],"is":[8,110,122,158,179],"important":[9],"for":[10,72],"understanding":[11],"molecular":[13],"mechanisms":[14],"life.":[16],"The":[17,44,114],"number":[18,98],"publicly":[20],"available":[21],"protein":[22,34,62,73,79,92,141],"has":[24],"increasingly":[25],"become":[26],"extremely":[27,167],"large.":[28],"Still,":[29],"classification":[31,60,70],"a":[33,37,68,82,111,125,185,190,197],"structure":[35,80],"remains":[36],"difficult,":[38],"costly,":[39],"time":[41],"consuming":[42],"task.":[43],"difficulties":[45],"are":[46],"often":[47],"due":[48],"to":[49,89,160,171,181,184,207],"essential":[51],"role":[52],"spatial":[54],"topological":[56,146],"in":[58,143,165,189,204],"structures.":[63],"RESULTS:":[64],"We":[65,149,174],"propose":[66],"ProtNN,":[67],"novel":[69],"approach":[71],"3D-structures.":[74],"Given":[75],"an":[76,152,166],"unannotated":[77],"query":[78,91,137],"set":[83],"annotated":[85,120],"proteins,":[86,107],"ProtNN":[87,157,178],"assigns":[88],"class":[94],"with":[95,193,196],"highest":[97],"votes":[100],"across":[101],"k":[103,109],"nearest":[104,118],"neighbor":[105,119],"reference":[106,140],"where":[108],"user-defined":[112],"parameter.":[113],"search":[115],"based":[123],"on":[124],"protein-graph":[126],"representation":[127],"model":[128],"pairwise":[130],"similarities":[131],"between":[132],"vector":[133],"embedding":[134],"structural":[144],"spaces.":[147],"CONCLUSIONS:":[148],"demonstrate":[150],"through":[151],"extensive":[153],"experimental":[154],"evaluation":[155],"that":[156,177],"able":[159,180],"accurately":[161],"classify":[162],"several":[163],"datasets":[164],"fast":[168],"runtime":[169,205],"compared":[170,206],"state-of-the-art":[172,208],"approaches.":[173,209],"further":[175],"show":[176],"scale":[182],"up":[183],"whole":[186],"PDB":[187],"dataset":[188],"single-process":[191],"mode":[192],"no":[194],"parallelization,":[195],"gain":[198],"thousands":[200],"order":[201],"magnitude":[203]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}