{"id":"https://openalex.org/W2131123685","doi":"https://doi.org/10.1093/bioinformatics/btt578","title":"FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking","display_name":"FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking","publication_year":2013,"publication_date":"2013-10-15","ids":{"openalex":"https://openalex.org/W2131123685","doi":"https://doi.org/10.1093/bioinformatics/btt578","mag":"2131123685","pmid":"https://pubmed.ncbi.nlm.nih.gov/24130308"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt578","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt578","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/660/17144812/btt578.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/660/17144812/btt578.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["SA","US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I185163786","https://openalex.org/I188891513","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066090493","display_name":"Lukasz Jaroszewski","orcid":null},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["SA","US"],"is_corresponding":false,"raw_author_name":"Lukasz Jaroszewski","raw_affiliation_strings":["1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I185163786","https://openalex.org/I188891513","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072166385","display_name":"Zhanwen Li","orcid":null},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["SA","US"],"is_corresponding":false,"raw_author_name":"Zhanwen Li","raw_affiliation_strings":["1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I185163786","https://openalex.org/I188891513","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010671148","display_name":"Adam Godzik","orcid":"https://orcid.org/0000-0002-2425-852X"},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["SA","US"],"is_corresponding":true,"raw_author_name":"Adam Godzik","raw_affiliation_strings":["1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, 2Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. La Jolla, CA 92093-0446, USA and 3Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I185163786","https://openalex.org/I188891513","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010671148"],"corresponding_institution_ids":["https://openalex.org/I185163786","https://openalex.org/I188891513","https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8902,"has_fulltext":false,"cited_by_count":125,"citation_normalized_percentile":{"value":0.91522336,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"30","issue":"5","first_page":"660","last_page":"667"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5794000029563904,"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":0.5794000029563904,"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":0.20520000159740448,"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":0.03200000151991844,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7732887864112854},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.712611198425293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5986154079437256},{"id":"https://openalex.org/keywords/structural-genomics","display_name":"Structural genomics","score":0.5758020877838135},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.5669502019882202},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5472930073738098},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.545520007610321},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.5268236994743347},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4877224862575531},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4666687548160553},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.46464961767196655},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.4643561840057373},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.46383652091026306},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4434088468551636},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4394407570362091},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.43306246399879456},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.4162740111351013},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40778958797454834},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.390951007604599},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.3361109495162964},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30540332198143005},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2077055275440216},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18792909383773804},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1518665850162506},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10555937886238098}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7732887864112854},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.712611198425293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5986154079437256},{"id":"https://openalex.org/C192772702","wikidata":"https://www.wikidata.org/wiki/Q2583975","display_name":"Structural genomics","level":3,"score":0.5758020877838135},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.5669502019882202},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5472930073738098},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.545520007610321},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.5268236994743347},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4877224862575531},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4666687548160553},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.46464961767196655},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.4643561840057373},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.46383652091026306},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4434088468551636},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4394407570362091},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.43306246399879456},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.4162740111351013},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40778958797454834},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.390951007604599},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.3361109495162964},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30540332198143005},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2077055275440216},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18792909383773804},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1518665850162506},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10555937886238098},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt578","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt578","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/660/17144812/btt578.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24130308","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24130308","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:escholarship.org:ark:/13030/qt7jx9v717","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7jx9v717","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 30, iss 5","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3306965","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3933871","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,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt578","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt578","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/660/17144812/btt578.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2856703182","display_name":null,"funder_award_id":"R01GM101457","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6080761528","display_name":null,"funder_award_id":"GM087218","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G805407378","display_name":null,"funder_award_id":"GM101457","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1498436455","https://openalex.org/W1965186869","https://openalex.org/W1970999032","https://openalex.org/W1978304263","https://openalex.org/W1996357466","https://openalex.org/W2008708467","https://openalex.org/W2011402521","https://openalex.org/W2036928610","https://openalex.org/W2051019453","https://openalex.org/W2052083266","https://openalex.org/W2065283382","https://openalex.org/W2079093876","https://openalex.org/W2085277871","https://openalex.org/W2087064593","https://openalex.org/W2102245393","https://openalex.org/W2110483430","https://openalex.org/W2115540209","https://openalex.org/W2125677968","https://openalex.org/W2130479394","https://openalex.org/W2144357990","https://openalex.org/W2145268834","https://openalex.org/W2146084306","https://openalex.org/W2147667050","https://openalex.org/W2151631782","https://openalex.org/W2153153865","https://openalex.org/W2153187042","https://openalex.org/W2156125289","https://openalex.org/W2157938277","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2167597940","https://openalex.org/W2170471837","https://openalex.org/W2171559274"],"related_works":["https://openalex.org/W4220937102","https://openalex.org/W4235583582","https://openalex.org/W4232453105","https://openalex.org/W1997379747","https://openalex.org/W1503558940","https://openalex.org/W2106883599","https://openalex.org/W2470147982","https://openalex.org/W1496233740","https://openalex.org/W1988384104","https://openalex.org/W1975453400"],"abstract_inverted_index":{"MOTIVATION:":[0],"Homology":[1],"detection":[2],"enables":[3],"grouping":[4],"proteins":[5],"into":[6],"families":[7,208],"and":[8,13,30,48,79,96,118,146,224],"prediction":[9,126],"of":[10,17,19,32,38,53,141,172,180,188,191,212,222],"their":[11],"structure":[12,125],"function.":[14],"The":[15,104],"range":[16],"application":[18],"homology-based":[20],"predictions":[21],"can":[22,194],"be":[23,195],"significantly":[24,163],"extended":[25],"by":[26,59],"using":[27,176],"sequence":[28],"profiles":[29],"incorporation":[31,37],"local":[33],"structural":[34,88],"features.":[35],"However,":[36],"the":[39,60,77,98,108,116,121,129,138,173,186],"latter":[40],"terms":[41],"varies":[42],"a":[43,101],"lot":[44],"between":[45],"existing":[46],"methods,":[47,62],"together":[49],"with":[50,100,120,156],"many":[51],"examples":[52],"distant":[54],"relations":[55],"not":[56,153,168,183],"recognized":[57],"even":[58],"best":[61],"suggests":[63],"that":[64,160],"further":[65],"improvements":[66,75],"are":[67,152],"still":[68],"possible.":[69],"RESULTS:":[70],"Here":[71],"we":[72],"describe":[73],"recent":[74],"to":[76,185,219],"fold":[78,147],"function":[80],"assignment":[81],"system":[82],"(FFAS)":[83],"method,":[84],"including":[85],"adding":[86],"optimized":[87],"features":[89,178],"(experimental":[90],"or":[91,210],"predicted),":[92],"'symmetrical'":[93],"Z-score":[94],"calculation":[95],"re-ranking":[97],"templates":[99],"neural":[102],"network.":[103],"alignment":[105],"accuracy":[106],"in":[107],"new":[109],"FFAS-3D":[110,132,150,166,193,230],"is":[111,231],"now":[112],"11%":[113],"higher":[114],"than":[115,200],"original":[117],"comparable":[119],"most":[122],"accurate":[123],"template-based":[124],"algorithms.":[127],"At":[128],"same":[130],"time,":[131],"has":[133],"high":[134],"success":[135],"rate":[136],"at":[137,233],"Structural":[139],"Classification":[140],"Proteins":[142],"(SCOP)":[143],"family,":[144],"superfamily":[145],"levels.":[148],"Importantly,":[149],"results":[151],"highly":[154],"correlated":[155],"other":[157,199],"programs":[158],"suggesting":[159],"it":[161],"may":[162],"improve":[164],"meta-predictions.":[165],"does":[167,182],"require":[169],"3D":[170],"structures":[171],"templates,":[174],"as":[175,206],"predicted":[177],"instead":[179],"structure-derived":[181],"lead":[184],"decrease":[187],"accuracy.":[189],"Because":[190],"that,":[192],"used":[196],"for":[197],"databases":[198],"Protein":[201,207],"Data":[202],"Bank":[203],"(PDB)":[204],"such":[205],"database":[209],"Clusters":[211],"orthologous":[213],"groups":[214],"thus":[215],"extending":[216],"its":[217],"applications":[218],"functional":[220],"annotations":[221],"genomes":[223],"protein":[225],"families.":[226],"AVAILABILITY":[227],"AND":[228],"IMPLEMENTATION:":[229],"available":[232],"http://ffas.godziklab.org.":[234]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":34},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":8}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}