{"id":"https://openalex.org/W3204560299","doi":"https://doi.org/10.34172/bi.2021.37","title":"GADP-align: A genetic algorithm and dynamic programming-based method for structural alignment of proteins","display_name":"GADP-align: A genetic algorithm and dynamic programming-based method for structural alignment of proteins","publication_year":2020,"publication_date":"2020-07-08","ids":{"openalex":"https://openalex.org/W3204560299","doi":"https://doi.org/10.34172/bi.2021.37","mag":"3204560299","pmid":"https://pubmed.ncbi.nlm.nih.gov/34631489","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8494253"},"language":"en","primary_location":{"id":"doi:10.34172/bi.2021.37","doi":"https://doi.org/10.34172/bi.2021.37","is_oa":true,"landing_page_url":"https://doi.org/10.34172/bi.2021.37","pdf_url":"https://bi.tbzmed.ac.ir/PDF/bi-11-271.pdf","source":{"id":"https://openalex.org/S4210202379","display_name":"Bioimpacts","issn_l":"2228-5652","issn":["2228-5652","2228-5660"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-70","russia-white-list-2"],"host_organization":"https://openalex.org/P4310319102","host_organization_name":"Tabriz University of Medical Sciences","host_organization_lineage":["https://openalex.org/P4310319102"],"host_organization_lineage_names":["Tabriz University of Medical Sciences"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioImpacts","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bi.tbzmed.ac.ir/PDF/bi-11-271.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036427469","display_name":"Soraya Mirzaei","orcid":"https://orcid.org/0000-0002-1994-3936","observed_orcids":["https://orcid.org/0000-0002-1994-3936"]},"institutions":[{"id":"https://openalex.org/I41832843","display_name":"University of Tabriz","ror":"https://ror.org/01papkj44","country_code":"IR","type":"education","lineage":["https://openalex.org/I41832843"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Soraya Mirzaei","raw_affiliation_strings":["Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran"],"raw_orcid":"https://orcid.org/0000-0002-1994-3936","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran","institution_ids":["https://openalex.org/I41832843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066720584","display_name":"Jafar Razmara","orcid":"https://orcid.org/0000-0002-6320-8517","observed_orcids":["https://orcid.org/0000-0002-6320-8517"]},"institutions":[{"id":"https://openalex.org/I41832843","display_name":"University of Tabriz","ror":"https://ror.org/01papkj44","country_code":"IR","type":"education","lineage":["https://openalex.org/I41832843"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Jafar Razmara","raw_affiliation_strings":["Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran"],"raw_orcid":"https://orcid.org/0000-0002-6320-8517","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran","institution_ids":["https://openalex.org/I41832843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084846786","display_name":"Shahriar Lotfi","orcid":"https://orcid.org/0000-0001-5460-3948","observed_orcids":["https://orcid.org/0000-0001-5460-3948"]},"institutions":[{"id":"https://openalex.org/I41832843","display_name":"University of Tabriz","ror":"https://ror.org/01papkj44","country_code":"IR","type":"education","lineage":["https://openalex.org/I41832843"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Shahriar Lotfi","raw_affiliation_strings":["Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran","institution_ids":["https://openalex.org/I41832843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066720584"],"corresponding_institution_ids":["https://openalex.org/I41832843"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":96},"biblio":{"volume":"11","issue":"4","first_page":"271","last_page":"279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.98580002784729,"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":0.98580002784729,"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":0.007400000002235174,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0008999999845400453,"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/protein-structure-alignment","display_name":"protein structure alignment","score":0.8360000252723694},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"genetic algorithm","score":0.6510000228881836},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"dynamic programming","score":0.8370000123977661},{"id":"https://openalex.org/keywords/hybrid-optimization","display_name":"hybrid optimization","score":0.7689999938011169},{"id":"https://openalex.org/keywords/secondary-structure-elements","display_name":"secondary structure elements","score":0.953000009059906},{"id":"https://openalex.org/keywords/local-optima-avoidance","display_name":"local optima avoidance","score":0.7279999852180481},{"id":"https://openalex.org/keywords/global-alignment","display_name":"global alignment","score":0.6570000052452087}],"concepts":[{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.8009423613548279},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6399030685424805},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6334490180015564},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.6066775321960449},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5986582040786743},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.59195476770401},{"id":"https://openalex.org/C110332635","wikidata":"https://www.wikidata.org/wiki/Q629498","display_name":"Genetic programming","level":2,"score":0.48536407947540283},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.47658202052116394},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4195062816143036},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.28796783089637756},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18915411829948425},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.11898970603942871},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.07832899689674377},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.34172/bi.2021.37","doi":"https://doi.org/10.34172/bi.2021.37","is_oa":true,"landing_page_url":"https://doi.org/10.34172/bi.2021.37","pdf_url":"https://bi.tbzmed.ac.ir/PDF/bi-11-271.pdf","source":{"id":"https://openalex.org/S4210202379","display_name":"Bioimpacts","issn_l":"2228-5652","issn":["2228-5652","2228-5660"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-70","russia-white-list-2"],"host_organization":"https://openalex.org/P4310319102","host_organization_name":"Tabriz University of Medical Sciences","host_organization_lineage":["https://openalex.org/P4310319102"],"host_organization_lineage_names":["Tabriz University of Medical Sciences"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioImpacts","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:7391587","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8494253","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmid:34631489","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34631489","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,"listed_in":[],"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":"BioImpacts : BI","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8494253","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8494253/","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,"listed_in":[],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioimpacts","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:eee73badd18c46bd9c8e6b560dcdd985","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/eee73badd18c46bd9c8e6b560dcdd985","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioImpacts, Vol 11, Iss 4, Pp 271-279 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.34172/bi.2021.37","doi":"https://doi.org/10.34172/bi.2021.37","is_oa":true,"landing_page_url":"https://doi.org/10.34172/bi.2021.37","pdf_url":"https://bi.tbzmed.ac.ir/PDF/bi-11-271.pdf","source":{"id":"https://openalex.org/S4210202379","display_name":"Bioimpacts","issn_l":"2228-5652","issn":["2228-5652","2228-5660"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-70","russia-white-list-2"],"host_organization":"https://openalex.org/P4310319102","host_organization_name":"Tabriz University of Medical Sciences","host_organization_lineage":["https://openalex.org/P4310319102"],"host_organization_lineage_names":["Tabriz University of Medical Sciences"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioImpacts","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3204560299.pdf","grobid_xml":"https://content.openalex.org/works/W3204560299.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W314988462","https://openalex.org/W1559074274","https://openalex.org/W1582965838","https://openalex.org/W1801992990","https://openalex.org/W1966521833","https://openalex.org/W1978113501","https://openalex.org/W1978273076","https://openalex.org/W1999569420","https://openalex.org/W2005647400","https://openalex.org/W2009836662","https://openalex.org/W2013025153","https://openalex.org/W2022058405","https://openalex.org/W2031054122","https://openalex.org/W2053281575","https://openalex.org/W2074231493","https://openalex.org/W2102015425","https://openalex.org/W2102245393","https://openalex.org/W2102475449","https://openalex.org/W2104812418","https://openalex.org/W2108107014","https://openalex.org/W2128704599","https://openalex.org/W2147145103","https://openalex.org/W2152326664","https://openalex.org/W2161899160","https://openalex.org/W2167338363","https://openalex.org/W2172156899","https://openalex.org/W2271700264","https://openalex.org/W2409138684","https://openalex.org/W2518338066","https://openalex.org/W2897002272","https://openalex.org/W2913039147","https://openalex.org/W2979862754"],"related_works":["https://openalex.org/W2127054268","https://openalex.org/W2125083705","https://openalex.org/W2013025153","https://openalex.org/W2097471670","https://openalex.org/W89239075","https://openalex.org/W2019012247","https://openalex.org/W2156160803","https://openalex.org/W3010459429","https://openalex.org/W7100210684","https://openalex.org/W144180450"],"abstract_inverted_index":{"Introduction:":[0],"Similarity":[1],"analysis":[2],"of":[3,34,104,111,190,197],"protein":[4,68,143,218],"structure":[5,69,108],"is":[6,26,53,62,125],"considered":[7],"as":[8],"a":[9,48,59,80,85,115,217],"fundamental":[10],"step":[11,22],"to":[12,37,127,137,141,147],"give":[13],"insight":[14],"into":[15],"the":[16,29,39,97,129,156,167,171,176,180,186,191,203,208,222],"relationships":[17],"between":[18,32,50,106,216],"proteins.":[19,113],"The":[20,71,132,151,195],"primary":[21],"in":[23,145,164,228],"structural":[24],"alignment":[25,78,224],"looking":[27],"for":[28,45,66,75],"optimal":[30,77,182],"correspondence":[31,49,105],"residues":[33],"two":[35,51,112],"structures":[36,52],"optimize":[38,128],"scoring":[40],"function.":[41],"An":[42],"exhaustive":[43],"search":[44],"finding":[46],"such":[47],"intractable.":[54],"Methods:":[55],"In":[56],"this":[57,95,198],"paper,":[58],"hybrid":[60,81,158],"method":[61,73,82,98,159,178],"proposed,":[63],"namely":[64],"GADP-align,":[65],"pairwise":[67],"alignment.":[70,130],"proposed":[72,157,177],"looks":[74],"an":[76,89,101,120],"using":[79,169],"based":[83],"on":[84],"genetic":[86,116,204],"algorithm":[87,117,124,134,205],"and":[88,225],"iterative":[90,121],"dynamic":[91,122,172,209],"programming":[92,123,173,210],"technique.":[93,174],"To":[94],"end,":[96],"first":[99],"creates":[100],"initial":[102,188],"map":[103],"secondary":[107],"elements":[109],"(SSEs)":[110],"Then,":[114],"combined":[118],"with":[119,166,207],"employed":[126,136],"Results:":[131],"GADP-align":[133],"was":[135],"align":[138],"10":[139],"\u2018difficult":[140],"align\u2019":[142],"pairs":[144],"order":[146],"evaluate":[148],"its":[149],"performance.":[150],"experimental":[152],"study":[153],"shows":[154],"that":[155,201],"produces":[160],"highly":[161,213],"accurate":[162,214],"alignments":[163,215],"comparison":[165],"methods":[168],"exactly":[170],"Furthermore,":[175],"prevents":[179],"local":[181,229],"traps":[183],"caused":[184],"by":[185,220],"unsuitable":[187],"guess":[189],"corresponding":[192],"residues.":[193],"Conclusion:":[194],"findings":[196],"paper":[199],"demonstrate":[200],"employing":[202],"along":[206],"technique":[211],"yields":[212],"pair":[219],"exploring":[221],"global":[223],"avoiding":[226],"trapping":[227],"alignments.":[230]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2021-10-11T00:00:00"}