{"id":"https://openalex.org/W4410139041","doi":"https://doi.org/10.1093/bioinformatics/btaf277","title":"Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning","display_name":"Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410139041","doi":"https://doi.org/10.1093/bioinformatics/btaf277","pmid":"https://pubmed.ncbi.nlm.nih.gov/40326701"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf277","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf277","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf277","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012569393","display_name":"Shaun M. Kandathil","orcid":"https://orcid.org/0000-0002-2671-2140"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shaun M Kandathil","raw_affiliation_strings":["Department of Computer Science, University College London , London WC1E 6BT,","University College London Department of Computer Science, , London, WC1E 6BT,","University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,"],"raw_orcid":"https://orcid.org/0000-0002-2671-2140","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London , London WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Department of Computer Science, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065901458","display_name":"Andy M. Lau","orcid":"https://orcid.org/0000-0003-0572-7826"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andy M Lau","raw_affiliation_strings":["Department of Computer Science, University College London , London WC1E 6BT,","University College London Department of Computer Science, , London, WC1E 6BT,","University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London , London WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Department of Computer Science, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087098726","display_name":"Daniel Buchan","orcid":"https://orcid.org/0000-0001-7391-4696"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel W A Buchan","raw_affiliation_strings":["Department of Computer Science, University College London , London WC1E 6BT,","University College London Department of Computer Science, , London, WC1E 6BT,","University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,"],"raw_orcid":"https://orcid.org/0000-0001-7391-4696","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London , London WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Department of Computer Science, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068654082","display_name":"David T. Jones","orcid":"https://orcid.org/0000-0001-8626-3765"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"David T Jones","raw_affiliation_strings":["Department of Computer Science, University College London , London WC1E 6BT,","Institute of Structural and Molecular Biology, University College London , London WC1E 6BT,","University College London Department of Computer Science, , London, WC1E 6BT,","University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,"],"raw_orcid":"https://orcid.org/0000-0001-8626-3765","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London , London WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Institute of Structural and Molecular Biology, University College London , London WC1E 6BT,","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Department of Computer Science, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"University College London Institue of Structural and Molecular Biology, , London, WC1E 6BT,","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5068654082"],"corresponding_institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.0369,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.86180136,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"41","issue":"5","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":0.48030000925064087,"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":0.48030000925064087,"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":0.08399999886751175,"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":0.08370000123977661,"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":0.7693778276443481},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.657263457775116},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6295595169067383},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.62843257188797},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5576406121253967},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.540547788143158},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5011868476867676},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.4241005480289459},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.4144771099090576},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.39009571075439453},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35097166895866394},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1963118612766266},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.18967100977897644},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11228257417678833},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.09137970209121704}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7693778276443481},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.657263457775116},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6295595169067383},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.62843257188797},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5576406121253967},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.540547788143158},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5011868476867676},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.4241005480289459},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.4144771099090576},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39009571075439453},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35097166895866394},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1963118612766266},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.18967100977897644},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11228257417678833},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.09137970209121704},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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:10.1093/bioinformatics/btaf277","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf277","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40326701","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40326701","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12122203","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12122203","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf277","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf277","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7514653848","display_name":"Accelerating and enhancing the PSIPRED Workbench with deep learning","funder_award_id":"BB/T019379/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7912758743","display_name":"Accelerating and enhancing the PSIPRED Workbench with deep learning","funder_award_id":"BB/T019409/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8793249621","display_name":"Exploiting Differentiable Programming Models For Protein Structure Prediction And Modelling","funder_award_id":"BB/W008556/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1510161841","https://openalex.org/W1965827393","https://openalex.org/W2102245393","https://openalex.org/W2579272540","https://openalex.org/W2941112903","https://openalex.org/W2950954328","https://openalex.org/W2984761660","https://openalex.org/W3106745904","https://openalex.org/W3115809040","https://openalex.org/W3177828909","https://openalex.org/W4287325738","https://openalex.org/W4319004578","https://openalex.org/W4319048420","https://openalex.org/W4327550249","https://openalex.org/W4375858802","https://openalex.org/W4386496033","https://openalex.org/W4389947479","https://openalex.org/W4396936937","https://openalex.org/W4403925091","https://openalex.org/W4409217924"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W2037549926","https://openalex.org/W2345479200","https://openalex.org/W2183306018","https://openalex.org/W2849310602","https://openalex.org/W3006008237","https://openalex.org/W2366671346","https://openalex.org/W1783960894","https://openalex.org/W375236608","https://openalex.org/W1970949629"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,196],"availability":[2],"of":[3,7,31,71,120,166,180],"very":[4],"large":[5],"numbers":[6],"protein":[8,65],"structures":[9,33,98],"from":[10,163],"accurate":[11],"computational":[12],"methods":[13],"poses":[14],"new":[15],"challenges":[16,40,50],"in":[17,34,199],"storing,":[18],"searching":[19],"and":[20,101,129,133,190],"detecting":[21],"relationships":[22],"between":[23,64],"these":[24,49,171],"structures.":[25],"In":[26,77],"particular,":[27],"the":[28,35,69,110,118,137,164,178,211],"new-found":[29],"abundance":[30],"multi-domain":[32,96],"AlphaFold":[36],"structure":[37,43,55],"database":[38,107],"introduces":[39],"for":[41,74,113,148],"traditional":[42],"comparison":[44,56],"methods.":[45],"RESULTS:":[46],"We":[47,67,168],"address":[48],"using":[51,177],"a":[52,80,104],"fast,":[53],"embedding-based":[54],"method":[57],"called":[58],"Foldclass":[59,72,105,130,189],"which":[60,93],"detects":[61],"structural":[62,182],"similarity":[63],"domains.":[66],"demonstrate":[68],"accuracy":[70],"embeddings":[73],"homology":[75],"detection.":[76],"combination":[78],"with":[79],"recently":[81],"developed":[82],"deep":[83],"learning-based":[84],"automatic":[85],"domain":[86],"segmentation":[87],"tool":[88,139],"Merizo,":[89],"we":[90],"develop":[91],"Merizo-search,":[92],"first":[94],"segments":[95],"query":[97],"into":[99,127],"domains,":[100,128,136],"then":[102],"searches":[103],"embedding":[106],"to":[108,122,131,143,157],"determine":[109],"top":[111],"matches":[112],"each":[114],"constituent":[115],"domain.":[116],"Combining":[117],"ability":[119],"Merizo":[121],"accurately":[123],"segment":[124],"complete":[125,149],"chains":[126],"embed":[132],"detect":[134,145],"similar":[135],"Merizo-search":[138,191,206],"can":[140],"be":[141],"used":[142,198],"rapidly":[144],"per-domain":[146],"similarities":[147],"chains,":[150],"taking":[151],"as":[152,154],"little":[153],"2":[155],"min":[156],"search":[158],"all":[159],"365":[160],"million":[161],"domains":[162],"Encyclopedia":[165],"Domains.":[167],"anticipate":[169],"that":[170],"tools":[172],"will":[173],"enable":[174],"many":[175],"analyses":[176],"wealth":[179],"predicted":[181],"data":[183],"now":[184],"available.":[185],"AVAILABILITY":[186],"AND":[187],"IMPLEMENTATION:":[188],"are":[192],"available":[193,209],"at":[194,204,215],"https://github.com/psipred/merizo_search.":[195],"version":[197],"this":[200],"publication":[201],"is":[202,207],"archived":[203],"https://doi.org/10.5281/zenodo.15120830.":[205],"also":[208],"on":[210],"PSIPRED":[212],"web":[213],"server":[214],"http://bioinf.cs.ucl.ac.uk/psipred.":[216]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
