{"id":"https://openalex.org/W1967538863","doi":"https://doi.org/10.1371/journal.pcbi.0040010","title":"Matt: Local Flexibility Aids Protein Multiple Structure Alignment","display_name":"Matt: Local Flexibility Aids Protein Multiple Structure Alignment","publication_year":2008,"publication_date":"2008-01-08","ids":{"openalex":"https://openalex.org/W1967538863","doi":"https://doi.org/10.1371/journal.pcbi.0040010","mag":"1967538863","pmid":"https://pubmed.ncbi.nlm.nih.gov/18193941"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0040010","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0040010","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040010&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040010&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086171822","display_name":"Matthew Menke","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Menke","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044078921","display_name":"Bonnie Berger","orcid":"https://orcid.org/0000-0002-2724-7228"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bonnie Berger","raw_affiliation_strings":["","Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"","institution_ids":[]},{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026411021","display_name":"Lenore Cowen","orcid":"https://orcid.org/0000-0001-6698-6413"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lenore Cowen","raw_affiliation_strings":["Department of Computer Science, Tufts University, Medford, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tufts University, Medford, Massachusetts, United States of America","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5026411021","https://openalex.org/A5044078921"],"corresponding_institution_ids":["https://openalex.org/I121934306","https://openalex.org/I63966007"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":8.9253,"has_fulltext":true,"cited_by_count":217,"citation_normalized_percentile":{"value":0.98570986,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"4","issue":"1","first_page":"e10","last_page":"e10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9980999827384949,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9980999827384949,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9943000078201294,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chaining","display_name":"Chaining","score":0.7759112119674683},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.7078975439071655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.65242999792099},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.6136376857757568},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.546928882598877},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5118305087089539},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4726088345050812},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.46101701259613037},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.4586503505706787},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.43781739473342896},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.42737269401550293},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4237295389175415},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41879022121429443},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.41829726099967957},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36105406284332275},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2392076849937439},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1960088610649109},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16591385006904602},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10221225023269653}],"concepts":[{"id":"https://openalex.org/C49020025","wikidata":"https://www.wikidata.org/wiki/Q1059099","display_name":"Chaining","level":2,"score":0.7759112119674683},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.7078975439071655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.65242999792099},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.6136376857757568},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.546928882598877},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5118305087089539},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4726088345050812},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.46101701259613037},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.4586503505706787},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.43781739473342896},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.42737269401550293},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4237295389175415},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41879022121429443},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.41829726099967957},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36105406284332275},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2392076849937439},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1960088610649109},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16591385006904602},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10221225023269653},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"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/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","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":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.0040010","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0040010","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040010&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18193941","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18193941","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.285.4949","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.285.4949","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/a4/4a/PLoS_Comput_Biol_2008_Jan_11_4(1)_e10.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:0040010","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0040010","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:aee4da9a77ce40aa8a35b27dc660fcbd","is_oa":true,"landing_page_url":"https://doaj.org/article/aee4da9a77ce40aa8a35b27dc660fcbd","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 1, p e10 (2008)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2622519","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC2186361","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2186361","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2186361","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0040010","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0040010","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040010&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G4392058819","display_name":"ITR-(ASE+NHS)-(dmc): Rational Genomic Annotation Systems: Integration, Mining and Modeling of Biological Data","funder_award_id":"0428715","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1967538863.pdf","grobid_xml":"https://content.openalex.org/works/W1967538863.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1508885706","https://openalex.org/W1527979595","https://openalex.org/W1559074274","https://openalex.org/W1801992990","https://openalex.org/W1916412816","https://openalex.org/W1965907701","https://openalex.org/W1966521833","https://openalex.org/W1969663541","https://openalex.org/W1971458166","https://openalex.org/W1973503184","https://openalex.org/W1978273076","https://openalex.org/W1981575795","https://openalex.org/W2002638840","https://openalex.org/W2004178884","https://openalex.org/W2005049999","https://openalex.org/W2015642465","https://openalex.org/W2019268215","https://openalex.org/W2031901496","https://openalex.org/W2033339460","https://openalex.org/W2036928610","https://openalex.org/W2038705005","https://openalex.org/W2040644205","https://openalex.org/W2042516820","https://openalex.org/W2085277871","https://openalex.org/W2087151779","https://openalex.org/W2087254300","https://openalex.org/W2095157453","https://openalex.org/W2097642323","https://openalex.org/W2098223336","https://openalex.org/W2101220662","https://openalex.org/W2108107014","https://openalex.org/W2108138353","https://openalex.org/W2110397834","https://openalex.org/W2115451817","https://openalex.org/W2127122014","https://openalex.org/W2137146016","https://openalex.org/W2137796207","https://openalex.org/W2141173210","https://openalex.org/W2143292980","https://openalex.org/W2144333666","https://openalex.org/W2147752484","https://openalex.org/W2149301682","https://openalex.org/W2152326664","https://openalex.org/W2157242929","https://openalex.org/W2168211076","https://openalex.org/W2168964504","https://openalex.org/W4232948691"],"related_works":["https://openalex.org/W1482324242","https://openalex.org/W2051969447","https://openalex.org/W2187357871","https://openalex.org/W1989090710","https://openalex.org/W2111937814","https://openalex.org/W1994518388","https://openalex.org/W2084367350","https://openalex.org/W1741740882","https://openalex.org/W24291664","https://openalex.org/W2005647400"],"abstract_inverted_index":{"Even":[0],"when":[1],"there":[2],"is":[3,20,30,143,152,155,176,267,294],"agreement":[4],"on":[5,165,182,189,277],"what":[6],"measure":[7],"a":[8,77,132,191,231,273],"protein":[9,74,161,302],"multiple":[10,160,194],"structure":[11,162,195,224,257],"alignment":[12,19,52,151,163,225],"should":[13],"be":[14,251],"optimizing,":[15],"finding":[16],"the":[17,41,50,83,146,150,166,179,186,213,239,278,281,305],"optimal":[18],"computationally":[21],"prohibitive.":[22],"One":[23],"approach":[24],"used":[25,252],"by":[26,137],"many":[27],"previous":[28],"methods":[29],"aligned":[31,44,93,118],"fragment":[32,94],"pair":[33,95],"chaining,":[34],"where":[35],"short":[36],"structural":[37,232],"fragments":[38,119],"from":[39,259,300,316],"all":[40],"proteins":[42,198,262,321],"are":[43,111,124,264],"against":[45,157],"each":[46],"other":[47,158,180,187],"optimally,":[48],"and":[49,61,90,109,169,217,284],"final":[51,147],"chains":[53],"these":[54,138],"together":[55],"in":[56,76,99,145,304,322,337],"geometrically":[57],"consistent":[58],"ways.":[59],"Ye":[60],"Godzik":[62],"have":[63],"recently":[64],"suggested":[65],"that":[66,263,311],"adding":[67],"geometric":[68,141],"flexibility":[69,104],"may":[70],"help":[71,229],"better":[72,211],"model":[73,320,334],"structures":[75,303],"variety":[78],"of":[79,117,193,197,215,222,246,261,280,291],"contexts.":[80],"We":[81,309],"introduce":[82],"program":[84,226],"Matt":[85,154,206,248,292],"(Multiple":[86],"Alignment":[87],"with":[88,178,199],"Translations":[89],"Twists),":[91],"an":[92,208,219],"chaining":[96],"algorithm":[97],"that,":[98],"intermediate":[100],"steps,":[101],"allows":[102],"local":[103],"between":[105],"fragments:":[106],"small":[107],"translations":[108],"rotations":[110],"temporarily":[112],"allowed":[113],"to":[114,210,228,238,253,296,319,333],"bring":[115],"sets":[116],"closer,":[120],"even":[121,328],"if":[122],"they":[123],"physically":[125],"impossible":[126],"under":[127],"rigid":[128],"body":[129],"transformations.":[130],"After":[131],"dynamic":[133],"programming":[134],"assembly":[135],"guided":[136],"\"bent\"":[139],"alignments,":[140],"consistency":[142],"restored":[144],"step":[148],"before":[149],"output.":[153],"tested":[156],"recent":[159],"programs":[164,181,188],"popular":[167],"Homstrad":[168],"SABmark":[170,306],"benchmark":[171,192,307],"datasets.":[172],"Matt's":[173,312],"global":[174],"performance":[175,314],"competitive":[177],"Homstrad,":[183],"but":[184],"outperforms":[185],"SABmark,":[190],"alignments":[196,249,293],"more":[200,329,338],"distant":[201],"homology.":[202],"On":[203],"both":[204],"datasets,":[205],"demonstrates":[207],"ability":[209,318,332],"align":[212],"ends":[214],"alpha-helices":[216],"beta-strands,":[218],"important":[220],"characteristic":[221],"any":[223],"intended":[227],"construct":[230],"template":[233],"library":[234],"for":[235],"threading":[236],"approaches":[237],"inverse":[240],"protein-folding":[241],"problem.":[242],"The":[243],"related":[244,340],"question":[245],"whether":[247],"can":[250],"distinguish":[254],"distantly":[255,339],"homologous":[256,266,301],"pairs":[258,260],"not":[265],"also":[268],"considered.":[269],"For":[270],"this":[271],"purpose,":[272],"p-value":[274],"score":[275],"based":[276],"length":[279],"common":[282],"core":[283],"average":[285],"root":[286],"mean":[287],"squared":[288],"deviation":[289],"(RMSD)":[290],"shown":[295],"largely":[297],"separate":[298],"decoys":[299],"dataset.":[308],"postulate":[310],"strong":[313],"comes":[315],"its":[317,331],"different":[323],"conformational":[324],"states":[325],"and,":[326],"perhaps":[327],"important,":[330],"backbone":[335],"distortions":[336],"proteins.":[341]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":22},{"year":2013,"cited_by_count":21},{"year":2012,"cited_by_count":19}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
