{"id":"https://openalex.org/W47596674","doi":null,"title":"Novel techniques for protein structure characterization using graph representation of proteins","display_name":"Novel techniques for protein structure characterization using graph representation of proteins","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W47596674","mag":"47596674"},"language":"en","primary_location":{"id":"pmh:oai:research.sabanciuniv.edu:16328","doi":null,"is_oa":false,"landing_page_url":"https://research.sabanciuniv.edu/id/eprint/16328/1/AlperKucukural.pdf","pdf_url":"https://research.sabanciuniv.edu/id/eprint/16328/1/AlperKucukural.pdf","source":{"id":"https://openalex.org/S4306402254","display_name":"Sabanci University","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I134235054","host_organization_name":"Sabanc\u0131 \u00dcniversitesi","host_organization_lineage":["https://openalex.org/I134235054"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"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/A5033094491","display_name":"Alper K\u00fc\u00e7\u00fckural","orcid":"https://orcid.org/0000-0001-9983-394X","observed_orcids":["https://orcid.org/0000-0001-9983-394X"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Alper K\u00fc\u00e7\u00fckural","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5033094491"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9657999873161316,"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":0.9657999873161316,"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":0.007199999876320362,"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":0.006599999964237213,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/protein-structure-characterization","display_name":"protein structural characterization","score":0.7379999756813049},{"id":"https://openalex.org/keywords/protein-fold-prediction","display_name":"protein fold prediction","score":0.5889999866485596},{"id":"https://openalex.org/keywords/protein-function-annotation","display_name":"protein annotation","score":0.5789999961853027},{"id":"https://openalex.org/keywords/protein-domain-prediction","display_name":"protein domain prediction","score":0.8320000171661377},{"id":"https://openalex.org/keywords/protein-fold-classification","display_name":"protein fold classification","score":0.6980000138282776},{"id":"https://openalex.org/keywords/protein-threading","display_name":"protein threading","score":0.6169999837875366},{"id":"https://openalex.org/keywords/subgraph-matching","display_name":"subgraph matching","score":0.6700000166893005},{"id":"https://openalex.org/keywords/protein-structure-alignment","display_name":"protein structure alignment","score":0.5839999914169312},{"id":"https://openalex.org/keywords/protein-structure-comparison","display_name":"protein structure comparison","score":0.45399999618530273}],"concepts":[{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.6871627569198608},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5399999022483826},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.5346775054931641},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.52641361951828},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5205967426300049},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5181783437728882},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.5032629370689392},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.46781229972839355},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4187206029891968},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37983477115631104},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37502023577690125},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35586369037628174},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1949579119682312},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.18016931414604187},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14831888675689697},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1418963074684143},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:research.sabanciuniv.edu:16328","doi":null,"is_oa":false,"landing_page_url":"https://research.sabanciuniv.edu/id/eprint/16328/1/AlperKucukural.pdf","pdf_url":"https://research.sabanciuniv.edu/id/eprint/16328/1/AlperKucukural.pdf","source":{"id":"https://openalex.org/S4306402254","display_name":"Sabanci University","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I134235054","host_organization_name":"Sabanc\u0131 \u00dcniversitesi","host_organization_lineage":["https://openalex.org/I134235054"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:47596674","doi":null,"is_oa":false,"landing_page_url":"https://research.sabanciuniv.edu/16328/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W135031542","https://openalex.org/W1546433743","https://openalex.org/W1551403939","https://openalex.org/W1601937749","https://openalex.org/W1910918478","https://openalex.org/W1967623938","https://openalex.org/W1971937094","https://openalex.org/W1973555128","https://openalex.org/W1973761246","https://openalex.org/W1977004736","https://openalex.org/W1985241583","https://openalex.org/W1997199912","https://openalex.org/W2009836662","https://openalex.org/W2057483934","https://openalex.org/W2068886104","https://openalex.org/W2085764610","https://openalex.org/W2088534163","https://openalex.org/W2089467562","https://openalex.org/W2092577148","https://openalex.org/W2097542211","https://openalex.org/W2097651746","https://openalex.org/W2102245393","https://openalex.org/W2102333330","https://openalex.org/W2102673137","https://openalex.org/W2103150692","https://openalex.org/W2103717543","https://openalex.org/W2104873783","https://openalex.org/W2106030336","https://openalex.org/W2107110246","https://openalex.org/W2109109045","https://openalex.org/W2109197549","https://openalex.org/W2111586169","https://openalex.org/W2115595474","https://openalex.org/W2115799627","https://openalex.org/W2118347512","https://openalex.org/W2124637492","https://openalex.org/W2124908487","https://openalex.org/W2126359798","https://openalex.org/W2129448010","https://openalex.org/W2131655958","https://openalex.org/W2137659815","https://openalex.org/W2137955461","https://openalex.org/W2144258433","https://openalex.org/W2146940292","https://openalex.org/W2152326664","https://openalex.org/W2153463820","https://openalex.org/W2153504150","https://openalex.org/W2153953580","https://openalex.org/W2155480785","https://openalex.org/W2157236640","https://openalex.org/W2157938277","https://openalex.org/W2161337380","https://openalex.org/W2163333444","https://openalex.org/W2164154943","https://openalex.org/W2164243919","https://openalex.org/W2165023708","https://openalex.org/W2171602500","https://openalex.org/W2171707538","https://openalex.org/W3015634246","https://openalex.org/W4229940379"],"related_works":["https://openalex.org/W1605657707","https://openalex.org/W2187031168","https://openalex.org/W2480805937","https://openalex.org/W2260094152","https://openalex.org/W2895143973","https://openalex.org/W1768346236","https://openalex.org/W1982408277","https://openalex.org/W2057483934","https://openalex.org/W1527229042","https://openalex.org/W2971382890"],"abstract_inverted_index":{"Proteins":[0],"exhibit":[1],"an":[2],"infinite":[3],"variety":[4,123],"of":[5,11,24,50,88,107,124,163,187,206,245],"structures.":[6],"Around":[7],"50K":[8],"3D":[9],"structures":[10,60,189],"proteins":[12,38,108,164],"exist":[13],"in":[14,40,58,126],"PDB":[15],"database":[16],"among":[17],"unlimited":[18],"possibilities.":[19],"The":[20,55,68],"three":[21],"dimensional":[22],"structure":[23,36,90],"a":[25,34,207,229],"protein":[26,53,59,72,130,188],"is":[27,47,110,200],"crucial":[28],"to":[29,112,169,180,202,221,243],"its":[30],"function.":[31],"Even":[32],"within":[33],"common":[35],"family,":[37],"vary":[39],"length,":[41],"size,":[42],"and":[43,85,92,137,165,172,184],"sequence.":[44],"This":[45],"variation":[46],"the":[48,89,144,153,204,223,246],"reflection":[49],"evolution":[51],"on":[52],"sequences.":[54],"intrinsic":[56],"information":[57,151],"can":[61,74,119,142],"be":[62,75,120],"captured":[63],"by":[64,147,190],"their":[65,78],"graph":[66,161,166,211],"representations.":[67],"structural":[69,79],"similarities":[70],"between":[71],"families":[73],"deduced":[76],"using":[77,114,148,191,197],"features":[80],"such":[81,128],"as":[82,129],"connectivity,":[83],"betweenness,":[84],"cliquishness.":[86],"Most":[87],"comparison":[91],"alignment":[93,196],"methods":[94,118,179],"use":[95],"all":[96],"atom":[97,105],"coordinates":[98],"that\u2019s":[99],"why":[100],"they":[101],"need":[102],"reliable":[103],"full":[104],"representation":[106],"which":[109],"difficult":[111],"obtain":[113],"experimental":[115],"methods.":[116],"These":[117],"used":[121,160,177,201],"for":[122,216],"problems":[125],"bioinformatics":[127],"fold":[131,138,225],"prediction,":[132,136],"function":[133,205],"annotation,":[134],"domain":[135,217],"classification.":[139],"Our":[140],"approach":[141],"capture":[143],"same":[145],"knowledge":[146],"much":[149],"less":[150],"from":[152],"actual":[154],"structure.":[155],"In":[156,219],"this":[157],"thesis,":[158],"we":[159,176,226],"representations":[162],"theoretical":[167],"properties":[168],"discriminate":[170],"native":[171],"non-native":[173],"proteins.":[174],"Then":[175],"these":[178,236],"find":[181,222],"out":[182],"overall":[183],"local":[185,195],"similarity":[186],"dynamic":[192,198],"programming.":[193],"Afterward,":[194],"programming":[199],"determine":[203],"protein.":[208],"Moreover,":[209],"sub":[210],"matching":[212],"algorithms":[213],"was":[214],"employed":[215],"prediction.":[218],"order":[220],"correct":[224],"also":[227],"developed":[228],"genetic":[230],"algorithm":[231],"based":[232],"threading":[233],"approach.":[234],"All":[235],"applications":[237],"gave":[238],"better":[239],"or":[240],"comparable":[241],"results":[242],"state":[244],"art.":[247]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}