{"id":"https://openalex.org/W2514829374","doi":"https://doi.org/10.1186/s12859-016-1199-y","title":"Evaluating the accuracy of protein design using native secondary sub-structures","display_name":"Evaluating the accuracy of protein design using native secondary sub-structures","publication_year":2016,"publication_date":"2016-09-05","ids":{"openalex":"https://openalex.org/W2514829374","doi":"https://doi.org/10.1186/s12859-016-1199-y","mag":"2514829374","pmid":"https://pubmed.ncbi.nlm.nih.gov/27597167"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1199-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1199-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1199-y","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/s12859-016-1199-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004214194","display_name":"Marziyeh Movahedi","orcid":null},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Marziyeh Movahedi","raw_affiliation_strings":["Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067478126","display_name":"Fatemeh Zare\u2010Mirakabad","orcid":"https://orcid.org/0000-0003-2849-3778"},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Fatemeh Zare-Mirakabad","raw_affiliation_strings":["Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran. f.zare@aut.ac.ir","Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran. f.zare@aut.ac.ir","institution_ids":[]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003496440","display_name":"Seyed Shahriar Arab","orcid":"https://orcid.org/0000-0002-2739-1617"},"institutions":[{"id":"https://openalex.org/I1516879","display_name":"Tarbiat Modares University","ror":"https://ror.org/03mwgfy56","country_code":"IR","type":"education","lineage":["https://openalex.org/I1516879"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Seyed Shahriar Arab","raw_affiliation_strings":["Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University (TMU), Tehran, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University (TMU), Tehran, Iran","institution_ids":["https://openalex.org/I1516879"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5004214194"],"corresponding_institution_ids":["https://openalex.org/I158248296"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3482,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.69097984,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"353","last_page":"353"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9088000059127808,"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":0.9088000059127808,"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":0.017500000074505806,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.00930000003427267,"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/dna-microarray","display_name":"DNA microarray","score":0.5716475248336792},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5348863005638123},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5253384113311768},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32445862889289856},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2892887592315674},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2218715250492096},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08832383155822754}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5716475248336792},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5348863005638123},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5253384113311768},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32445862889289856},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2892887592315674},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2218715250492096},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08832383155822754},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-016-1199-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1199-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1199-y","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:27597167","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27597167","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:5011913","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5011913","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/s12859-016-1199-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1199-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1199-y","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2514829374.pdf","grobid_xml":"https://content.openalex.org/works/W2514829374.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W24553703","https://openalex.org/W395144820","https://openalex.org/W1721447212","https://openalex.org/W1884233127","https://openalex.org/W1980471666","https://openalex.org/W1987134040","https://openalex.org/W1992426410","https://openalex.org/W1995824897","https://openalex.org/W1997325518","https://openalex.org/W1998138053","https://openalex.org/W2003229787","https://openalex.org/W2008708467","https://openalex.org/W2013136212","https://openalex.org/W2014374038","https://openalex.org/W2023490488","https://openalex.org/W2025146643","https://openalex.org/W2047094503","https://openalex.org/W2052422361","https://openalex.org/W2064106707","https://openalex.org/W2067598960","https://openalex.org/W2081208252","https://openalex.org/W2092087990","https://openalex.org/W2102245393","https://openalex.org/W2106775540","https://openalex.org/W2108107014","https://openalex.org/W2108664112","https://openalex.org/W2121125726","https://openalex.org/W2126719129","https://openalex.org/W2128653811","https://openalex.org/W2142529984","https://openalex.org/W2147905080","https://openalex.org/W2155201844","https://openalex.org/W2161151688","https://openalex.org/W2166912610","https://openalex.org/W2796936280","https://openalex.org/W4299669638","https://openalex.org/W4299702438"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"BACKGROUND:":[0],"According":[1],"to":[2,51,136,148,155,165,170,201,283],"structure-dependent":[3],"function":[4],"of":[5,25,44,62,93,197,204,210,239,252,260,267],"proteins,":[6],"two":[7],"main":[8],"challenging":[9],"problems":[10],"called":[11,179],"Protein":[12,18,100],"Structure":[13,102],"Prediction":[14],"(PSP)":[15],"and":[16,222,241,270,277],"Inverse":[17,103],"Folding":[19,104],"(IPF)":[20],"are":[21],"investigated.":[22],"In":[23,39,122,140,263],"spite":[24],"IPF":[26,45,281],"essential":[27],"applications,":[28],"it":[29,116],"has":[30],"not":[31,227],"been":[32],"investigated":[33],"as":[34,36,115,274],"much":[35],"PSP":[37],"problem.":[38,139],"fact,":[40,264],"the":[41,63,94,99,119,146,156,190,205,234,236,249,258,265],"ultimate":[42],"goal":[43],"problem":[46,106,282],"or":[47,57],"protein":[48,68,85,95,113,198],"design":[49,69,149],"is":[50,70,81,107,134,215],"create":[52],"proteins":[53,188],"with":[54,217],"enhanced":[55],"properties":[56],"even":[58],"novel":[59,126],"functions.":[60],"One":[61],"major":[64],"computational":[65],"challenges":[66],"in":[67,112,189],"its":[71],"large":[72],"sequence":[73],"space,":[74],"namely":[75],"searching":[76],"through":[77,233],"all":[78],"plausible":[79],"sequences":[80,153,212,243],"impossible.":[82],"Inasmuch":[83],"as,":[84],"secondary":[86,132,158,199,208],"structure":[87,209,231],"represents":[88],"an":[89,284],"appropriate":[90,150],"primary":[91],"scaffold":[92],"conformation,":[96],"undoubtedly":[97],"studying":[98],"Secondary":[101],"(PSSIF)":[105],"a":[108,125,195],"quantum":[109],"leap":[110],"forward":[111],"design,":[114],"can":[117,144,162,255,288],"reduce":[118],"search":[120],"space.":[121],"this":[123,268],"paper,":[124],"genetic":[127],"algorithm":[128,147,178],"which":[129],"uses":[130],"native":[131,240,253],"sub-structures":[133,200],"proposed":[135,177],"solve":[137],"PSSIF":[138],"essence,":[141],"evolutionary":[142,183,250],"information":[143,184,251,269],"lead":[145],"amino":[151],"acid":[152],"respective":[154],"target":[157],"structures.":[159,174],"Furthermore,":[160],"they":[161],"be":[163,289],"folded":[164],"tertiary":[166,230],"structures":[167,254],"almost":[168],"similar":[169],"their":[171],"reference":[172],"3D":[173],"RESULTS:":[175],"The":[176,207],"GAPSSIF":[180,214,287],"benefits":[181],"from":[182],"obtained":[185,219],"by":[186,213,220],"solved":[187],"PDB.":[191],"Therefore,":[192],"we":[193,225],"construct":[194],"repository":[196],"accelerate":[202],"convergence":[203],"algorithm.":[206],"designed":[211,242,261],"comparable":[216],"those":[218],"Evolver":[221],"EvoDesign.":[223],"Although":[224],"do":[226],"explicitly":[228],"consider":[229],"features":[232,272],"algorithm,":[235],"structural":[237],"similarity":[238],"declares":[244],"acceptable":[245],"values.":[246],"CONCLUSIONS:":[247],"Using":[248],"significantly":[256],"improve":[257],"quality":[259],"sequences.":[262],"combination":[266],"effective":[271],"such":[273],"solvent":[275],"accessibility":[276],"torsion":[278],"angles":[279],"leads":[280],"efficient":[285],"solution.":[286],"downloaded":[290],"at":[291],"http://bioinformatics.aut.ac.ir/GAPSSIF/":[292],".":[293]},"counts_by_year":[{"year":2021,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}