{"id":"https://openalex.org/W7126046605","doi":"https://doi.org/10.1109/bibm66473.2025.11356623","title":"A Comparative Performance Study of Protein Structure Alignment Tools on Homology Detection with Biological Relevance","display_name":"A Comparative Performance Study of Protein Structure Alignment Tools on Homology Detection with Biological Relevance","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126046605","doi":"https://doi.org/10.1109/bibm66473.2025.11356623"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356623","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356623","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5103926979","display_name":"Zhuoyang Chen","orcid":"https://orcid.org/0009-0007-1859-4571"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Zhuoyang Chen","raw_affiliation_strings":["The Hong Kong University of Science and Technology,Guangzhou"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology,Guangzhou","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101979633","display_name":"Xuechen Zhang","orcid":"https://orcid.org/0000-0002-6294-0781"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Xuechen Zhang","raw_affiliation_strings":["The Hong Kong University of Science and Technology"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology","institution_ids":["https://openalex.org/I200769079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053577648","display_name":"William W. Yu","orcid":"https://orcid.org/0000-0001-5354-6718"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Weichuan Yu","raw_affiliation_strings":["The Hong Kong University of Science and Technology"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology","institution_ids":["https://openalex.org/I200769079"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124156395","display_name":"Qiong Luo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qiong Luo","raw_affiliation_strings":["The Hong Kong University of Science and Technology,Guangzhou"],"affiliations":[{"raw_affiliation_string":"The Hong Kong University of Science and Technology,Guangzhou","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5103926979"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.65155732,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"134","last_page":"139"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6396999955177307,"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":0.6396999955177307,"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":0.10729999840259552,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.062199998646974564,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6577000021934509},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.6389999985694885},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5792999863624573},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5073999762535095},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.48179998993873596},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4620000123977661},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45559999346733093},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4447000026702881},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.38119998574256897},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.3702999949455261}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6804999709129333},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6577000021934509},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.6389999985694885},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6029999852180481},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5792999863624573},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5073999762535095},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.48179998993873596},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4620000123977661},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45559999346733093},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4447000026702881},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4203000068664551},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.38119998574256897},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.3702999949455261},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.36500000953674316},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.36410000920295715},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34380000829696655},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.3353999853134155},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.3330000042915344},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.328900009393692},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3271999955177307},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32260000705718994},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.3215999901294708},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.3147999942302704},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3089999854564667},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30720001459121704},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.27869999408721924},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.2732999920845032},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26589998602867126},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2646999955177307},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.26339998841285706},{"id":"https://openalex.org/C45475804","wikidata":"https://www.wikidata.org/wiki/Q6675846","display_name":"Loop modeling","level":4,"score":0.2583000063896179},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.25780001282691956},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.25540000200271606},{"id":"https://openalex.org/C192772702","wikidata":"https://www.wikidata.org/wiki/Q2583975","display_name":"Structural genomics","level":3,"score":0.2547999918460846},{"id":"https://openalex.org/C2984217123","wikidata":"https://www.wikidata.org/wiki/Q25099949","display_name":"Structure function","level":2,"score":0.25429999828338623},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.2538999915122986}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356623","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356623","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6110468061","display_name":null,"funder_award_id":"Z1056,3030_009,BGF.001.2023","funder_id":"https://openalex.org/F4320323537","funder_display_name":"Hong Kong University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320323537","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1985040965","https://openalex.org/W2040233577","https://openalex.org/W2090617952","https://openalex.org/W2097270746","https://openalex.org/W2102245393","https://openalex.org/W2109383908","https://openalex.org/W2206740991","https://openalex.org/W2377064860","https://openalex.org/W2902353954","https://openalex.org/W3045523101","https://openalex.org/W3177828909","https://openalex.org/W4297329014","https://openalex.org/W4309858927","https://openalex.org/W4375858802","https://openalex.org/W4379882058","https://openalex.org/W4386496033","https://openalex.org/W4386860638","https://openalex.org/W4388464011","https://openalex.org/W4411754098"],"related_works":[],"abstract_inverted_index":{"In":[0,67,93,109],"this":[1],"study,":[2],"we":[3],"investigate":[4],"the":[5,55,64,107,125,137,169,183,191],"performance":[6,178],"of":[7,161,171,185],"nine":[8],"protein":[9,186],"structure":[10,35,187],"alignment":[11,53,145,188],"tools":[12,24,189],"on":[13,75,156],"three":[14],"tasks:":[15],"superposition":[16],"derivation,":[17],"structural":[18,94,173],"classification,":[19,95],"and":[20,33,43,58,143,164,174,194],"function":[21,110],"inference.":[22],"These":[23],"include":[25,49],"(1)":[26],"traditional":[27,83],"sequential":[28],"methods":[29,54,97,113],"using":[30],"both":[31,162],"3D":[32],"2D":[34],"representations,":[36],"(2)":[37],"non-sequential":[38],"methods,":[39,42,72,85,150],"(3)":[40],"flexible":[41],"(4)":[44],"deep-learning":[45],"methods.":[46],"We":[47,62,127],"also":[48],"two":[50],"canonical":[51],"sequence":[52,91,102,120,175],"Needleman-Wunsch":[56],"algorithm":[57],"BLASTp,":[59],"as":[60,152],"baselines.":[61],"have":[63],"following":[65],"results:":[66],"deriving":[68],"superposition,":[69],"deep":[70,148],"learning":[71,149],"which":[73],"focus":[74],"library":[76],"search,":[77],"produce":[78],"less":[79],"accurate":[80],"patterns":[81],"than":[82,90,101,119],"pairwise":[84],"but":[86],"are":[87,98,196],"more":[88,115],"precise":[89],"alignment;":[92],"structure-based":[96,112],"much":[99],"better":[100],"alignment,":[103,121],"with":[104,122],"DALI":[105],"performing":[106],"best;":[108],"inference,":[111],"recover":[114],"functional":[116],"homology":[117],"hits":[118],"KPAX":[123],"recovering":[124],"most.":[126],"identify":[128],"key":[129],"factors":[130],"that":[131],"affect":[132],"performance,":[133],"including":[134],"scoring":[135],"metrics,":[136],"ability":[138],"to":[139],"capture":[140],"side-chain":[141],"information,":[142],"partial":[144],"mechanisms.":[146],"Notably,":[147],"such":[151],"Foldseek,":[153],"perform":[154],"well":[155],"large-scale":[157],"queries,":[158],"in":[159,190],"terms":[160],"speed":[163],"accuracy.":[165],"Our":[166],"findings":[167],"highlight":[168],"importance":[170],"integrating":[172],"data":[176,195],"for":[177],"benefits,":[179],"providing":[180],"insight":[181],"into":[182],"development":[184],"future.":[192],"Code":[193],"available":[197],"at":[198],"https://github.com/georgedashen/StructAlign":[199]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}