{"id":"https://openalex.org/W2170449429","doi":"https://doi.org/10.1093/bioinformatics/btv092","title":"AIDA: <i>ab initio</i> domain assembly for automated multi-domain protein structure prediction and domain\u2013domain interaction prediction","display_name":"AIDA: <i>ab initio</i> domain assembly for automated multi-domain protein structure prediction and domain\u2013domain interaction prediction","publication_year":2015,"publication_date":"2015-02-19","ids":{"openalex":"https://openalex.org/W2170449429","doi":"https://doi.org/10.1093/bioinformatics/btv092","mag":"2170449429","pmid":"https://pubmed.ncbi.nlm.nih.gov/25701568"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv092","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2098/49034617/bioinformatics_31_13_2098.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/31/13/2098/49034617/bioinformatics_31_13_2098.pdf","any_repository_has_fulltext":true},"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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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, USA, 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, Jeddah, 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":2.3432,"has_fulltext":false,"cited_by_count":65,"citation_normalized_percentile":{"value":0.89012795,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"31","issue":"13","first_page":"2098","last_page":"2105"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7080000042915344,"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":0.7080000042915344,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.050599999725818634,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.03480000048875809,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/domain","display_name":"Domain (mathematical analysis)","score":0.746177077293396},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7392930388450623},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.674983024597168},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.663343608379364},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5960828065872192},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.538054883480072},{"id":"https://openalex.org/keywords/casp","display_name":"CASP","score":0.4581136107444763},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4524187445640564},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4227445721626282},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.4217769503593445},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3665403723716736},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35968586802482605},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1850481927394867},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12654802203178406},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10571393370628357}],"concepts":[{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.746177077293396},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7392930388450623},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.674983024597168},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.663343608379364},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5960828065872192},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.538054883480072},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.4581136107444763},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4524187445640564},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4227445721626282},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4217769503593445},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3665403723716736},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35968586802482605},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1850481927394867},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12654802203178406},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10571393370628357},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv092","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2098/49034617/bioinformatics_31_13_2098.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:25701568","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25701568","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/qt2gh954sn","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/2gh954sn","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 31, iss 13","raw_type":"article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/13/2098","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/13/2098","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4481839","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4481839","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv092","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv092","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2098/49034617/bioinformatics_31_13_2098.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":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the 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/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/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335134","display_name":"National Institutes of Natural Sciences","ror":"https://ror.org/055n47h92"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170449429.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1546896179","https://openalex.org/W1982609064","https://openalex.org/W2003852785","https://openalex.org/W2016685368","https://openalex.org/W2020179762","https://openalex.org/W2046535373","https://openalex.org/W2060259273","https://openalex.org/W2065283382","https://openalex.org/W2065578811","https://openalex.org/W2106648157","https://openalex.org/W2106839046","https://openalex.org/W2115540209","https://openalex.org/W2125677968","https://openalex.org/W2130479394","https://openalex.org/W2130581715","https://openalex.org/W2131123685","https://openalex.org/W2142961247","https://openalex.org/W2144112190","https://openalex.org/W2145112957","https://openalex.org/W2147805410","https://openalex.org/W2153153865","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2161303529","https://openalex.org/W2163363312","https://openalex.org/W2169285320","https://openalex.org/W2171559274","https://openalex.org/W2408289238"],"related_works":["https://openalex.org/W2411847509","https://openalex.org/W2411998238","https://openalex.org/W2155233650","https://openalex.org/W3198923619","https://openalex.org/W2093959518","https://openalex.org/W2334085108","https://openalex.org/W3199799076","https://openalex.org/W2561391236","https://openalex.org/W2147472674","https://openalex.org/W3199104097"],"abstract_inverted_index":{"MOTIVATION:":[0],"Most":[1],"proteins":[2],"consist":[3],"of":[4,95,111,146,160],"multiple":[5],"domains,":[6,34],"independent":[7],"structural":[8],"and":[9],"evolutionary":[10],"units":[11],"that":[12,37,151],"are":[13,47,176,188],"often":[14,28,48],"reshuffled":[15],"in":[16,109],"genomic":[17],"rearrangements":[18],"to":[19,41,81],"form":[20],"new":[21],"protein":[22,46,67,138],"architectures.":[23],"Template-based":[24],"modeling":[25],"methods":[26],"can":[27,78,115],"detect":[29],"homologous":[30],"templates":[31,36],"for":[32,64,136,158,178],"individual":[33],"but":[35],"could":[38,154],"be":[39,79,155],"used":[40,174],"model":[42],"the":[43,71,98,121,127,171],"entire":[44],"query":[45],"not":[49],"available.":[50],"RESULTS:":[51],"We":[52],"have":[53],"developed":[54],"a":[55],"fast":[56],"docking":[57],"algorithm":[58],"ab":[59,72],"initio":[60,73],"domain":[61,100,117,152],"assembly":[62],"(AIDA)":[63],"assembling":[65],"multi-domain":[66,96],"structures,":[68],"guided":[69],"by":[70,120],"folding":[74],"potential.":[75],"This":[76],"approach":[77,132],"extended":[80],"discontinuous":[82],"domains":[83,85],"(i.e.":[84],"with":[86],"'inserted'":[87],"domains).":[88],"When":[89],"tested":[90],"on":[91],"experimentally":[92],"solved":[93],"structures":[94],"proteins,":[97],"relative":[99],"positions":[101],"were":[102],"accurately":[103],"found":[104],"among":[105],"top":[106],"5000":[107],"models":[108],"86%":[110],"cases.":[112],"AIDA":[113,166],"server":[114],"use":[116],"assignments":[118],"provided":[119,128],"user":[122],"or":[123],"predict":[124],"them":[125],"from":[126],"sequence.":[129],"The":[130,142,165],"latter":[131],"is":[133],"particularly":[134],"useful":[135],"automated":[137],"structure":[139],"prediction":[140],"servers.":[141],"blind":[143],"test":[144],"consisting":[145],"95":[147],"CASP10":[148],"targets":[149],"shows":[150],"boundaries":[153],"successfully":[156],"determined":[157],"97%":[159],"targets.":[161],"AVAILABILITY":[162],"AND":[163],"IMPLEMENTATION:":[164],"package":[167],"as":[168,170],"well":[169],"benchmark":[172],"sets":[173],"here":[175],"available":[177,189],"download":[179],"at":[180,190],"http://ffas.burnham.org/AIDA/.":[181],"CONTACT:":[182],"adam@sanfordburnham.org":[183],"SUPPLEMENTARY":[184],"INFORMATION:":[185],"Supplementary":[186],"data":[187],"Bioinformatics":[191],"online.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2016-06-24T00:00:00"}