{"id":"https://openalex.org/W2157540858","doi":"https://doi.org/10.1093/bioinformatics/btn438","title":"P<scp>redict</scp>-2<scp>nd</scp>: a tool for generalized protein local structure prediction","display_name":"P<scp>redict</scp>-2<scp>nd</scp>: a tool for generalized protein local structure prediction","publication_year":2008,"publication_date":"2008-08-30","ids":{"openalex":"https://openalex.org/W2157540858","doi":"https://doi.org/10.1093/bioinformatics/btn438","mag":"2157540858","pmid":"https://pubmed.ncbi.nlm.nih.gov/18757875"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn438","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn438","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/21/2453/49055258/bioinformatics_24_21_2453.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/24/21/2453/49055258/bioinformatics_24_21_2453.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061159882","display_name":"Sol Katzman","orcid":"https://orcid.org/0000-0002-1787-1246"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Sol Katzman","raw_affiliation_strings":["1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I185103710","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082405466","display_name":"Christian Barrett","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Christian Barrett","raw_affiliation_strings":["1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I185103710","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090019079","display_name":"Grant Thiltgen","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Grant Thiltgen","raw_affiliation_strings":["1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I185103710","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034118773","display_name":"Rachel Karchin","orcid":"https://orcid.org/0000-0002-5069-1239"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Rachel Karchin","raw_affiliation_strings":["1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I185103710","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059033237","display_name":"Kevin Karplus","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"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":["US"],"is_corresponding":true,"raw_author_name":"Kevin Karplus","raw_affiliation_strings":["1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, 2Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412 and 3Department of Biomedica Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I185103710","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059033237"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I185103710","https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.731,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.90718374,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"21","first_page":"2453","last_page":"2459"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7121000289916992,"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":0.7121000289916992,"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":0.15719999372959137,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.04809999838471413,"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/computer-science","display_name":"Computer science","score":0.6280086636543274},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6042169332504272},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.578176736831665},{"id":"https://openalex.org/keywords/local-optimum","display_name":"Local optimum","score":0.5717089176177979},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.5591591000556946},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5158571600914001},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49449798464775085},{"id":"https://openalex.org/keywords/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.4811047911643982},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.44672074913978577},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.42821168899536133},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3934330344200134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38154494762420654},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.23223531246185303},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1670362949371338},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12207821011543274}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6280086636543274},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6042169332504272},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.578176736831665},{"id":"https://openalex.org/C141934464","wikidata":"https://www.wikidata.org/wiki/Q3305386","display_name":"Local optimum","level":2,"score":0.5717089176177979},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.5591591000556946},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5158571600914001},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49449798464775085},{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.4811047911643982},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.44672074913978577},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.42821168899536133},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3934330344200134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38154494762420654},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.23223531246185303},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1670362949371338},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12207821011543274},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"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}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"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":"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn438","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn438","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/21/2453/49055258/bioinformatics_24_21_2453.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:18757875","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18757875","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:CiteSeerX.psu:10.1.1.153.4756","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.153.4756","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://cs.ucsc.edu/~karplus/papers/predict-2nd.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2732275","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2732275","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/btn438","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn438","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/21/2453/49055258/bioinformatics_24_21_2453.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/G321024167","display_name":null,"funder_award_id":"R01 GM068570","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1499450468","https://openalex.org/W1567468271","https://openalex.org/W1966041739","https://openalex.org/W1967112996","https://openalex.org/W1970999032","https://openalex.org/W1978520289","https://openalex.org/W1996073320","https://openalex.org/W1996159969","https://openalex.org/W2008708467","https://openalex.org/W2008922668","https://openalex.org/W2033746410","https://openalex.org/W2041369927","https://openalex.org/W2041877620","https://openalex.org/W2082120777","https://openalex.org/W2097555181","https://openalex.org/W2100981947","https://openalex.org/W2105801262","https://openalex.org/W2106066024","https://openalex.org/W2108212798","https://openalex.org/W2114107538","https://openalex.org/W2119821739","https://openalex.org/W2122665495","https://openalex.org/W2122945697","https://openalex.org/W2140992384","https://openalex.org/W2141216359","https://openalex.org/W2141920771","https://openalex.org/W2147905080","https://openalex.org/W2153153865","https://openalex.org/W2153187042","https://openalex.org/W2155972356","https://openalex.org/W2156628505","https://openalex.org/W2158714788","https://openalex.org/W2159280460","https://openalex.org/W2611400920","https://openalex.org/W3201606613","https://openalex.org/W4230638849","https://openalex.org/W4235000932","https://openalex.org/W4239510810","https://openalex.org/W4247866849","https://openalex.org/W6633880454","https://openalex.org/W6674463856","https://openalex.org/W6683118431"],"related_works":["https://openalex.org/W2221737924","https://openalex.org/W51493542","https://openalex.org/W2253761889","https://openalex.org/W2804736179","https://openalex.org/W4252453648","https://openalex.org/W107329556","https://openalex.org/W2915333504","https://openalex.org/W1533579197","https://openalex.org/W3127664026","https://openalex.org/W2149007706"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predictions":[1],"of":[2,21,26,31,66,81,119,123,132,212,222],"protein":[3,68,89],"local":[4,72,109,163],"structure,":[5],"derived":[6],"from":[7,187],"sequence":[8,45,204,225],"alignment":[9],"information":[10],"alone,":[11],"provide":[12],"visualization":[13],"tools":[14],"for":[15,62,235,251,262],"biologists":[16],"to":[17,44,60,107,194,200,205],"evaluate":[18],"the":[19,29,117,121,129,138,154,183,188,195,198,206,210,233,245],"importance":[20],"amino":[22],"acid":[23],"residue":[24],"positions":[25],"interest":[27],"in":[28,64,84,125,161,232],"absence":[30],"X-ray":[32],"crystal/NMR":[33],"structures":[34],"or":[35],"homology":[36,63],"models.":[37],"They":[38],"are":[39,264],"also":[40],"useful":[41],"as":[42,51,78,116],"inputs":[43,213],"analysis":[46],"and":[47,103,128,259],"modeling":[48],"tools,":[49],"such":[50,115],"hidden":[52],"Markov":[53],"models":[54],"(HMMs),":[55],"which":[56],"can":[57,75],"be":[58,76],"used":[59,77],"search":[61],"databases":[65],"known":[67],"structure.":[69,91],"In":[70],"addition,":[71],"structure":[73,110,242],"predictions":[74,234],"a":[79,95,202,223,227],"component":[80],"cost":[82],"functions":[83],"genetic":[85],"algorithms":[86],"that":[87,98,220],"predict":[88],"tertiary":[90],"We":[92,135,218],"have":[93,104,136],"developed":[94],"program":[96,196],"(predict-2nd)":[97],"trains":[99],"multilayer":[100],"neural":[101,156],"networks":[102,186,261],"applied":[105],"it":[106],"numerous":[108],"alphabets,":[111],"tuning":[112],"network":[113],"parameters":[114],"number":[118,122,211],"layers,":[120],"units":[124],"each":[126,133,150],"layer":[127],"window":[130,147],"sizes":[131,148],"layer.":[134,151],"had":[137],"most":[139],"success":[140],"with":[141,144,174,244],"four-layer":[142,155],"networks,":[143],"gradually":[145],"increasing":[146,209],"at":[149,254,266,274],"RESULTS:":[152],"Because":[153],"nets":[157],"occasionally":[158],"get":[159],"trapped":[160],"poor":[162],"optima,":[164],"our":[165],"training":[166,176,181],"protocol":[167],"now":[168],"uses":[169],"many":[170],"different":[171,237],"random":[172],"starts,":[173],"short":[175,189],"runs,":[177],"followed":[178],"by":[179,216],"more":[180],"on":[182],"best":[184],"performing":[185],"runs.":[190],"One":[191],"recent":[192],"addition":[193],"is":[197,249,272],"option":[199],"add":[201],"guide":[203,224],"profile":[207],"inputs,":[208],"per":[214],"position":[215],"20.":[217],"find":[219],"use":[221,252],"provides":[226],"small":[228],"but":[229],"consistent":[230],"improvement":[231],"several":[236],"local-structure":[238],"alphabets.":[239],"AVAILABILITY:":[240],"Local":[241],"prediction":[243],"methods":[246],"described":[247],"here":[248],"available":[250,265,273],"online":[253],"http://www.soe.ucsc.edu/compbio/SAM_T08/T08-query.html.":[255],"The":[256],"source":[257],"code":[258],"example":[260],"PREDICT-2ND":[263],"http://www.soe.ucsc.edu/~karplus/predict-2nd/":[267],"A":[268],"required":[269],"C++":[270],"library":[271],"http://www.soe.ucsc.edu/~karplus/ultimate/":[275]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2016-06-24T00:00:00"}
