{"id":"https://openalex.org/W2067852761","doi":"https://doi.org/10.1186/1471-2105-9-531","title":"Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score","display_name":"Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score","publication_year":2008,"publication_date":"2008-12-01","ids":{"openalex":"https://openalex.org/W2067852761","doi":"https://doi.org/10.1186/1471-2105-9-531","mag":"2067852761","pmid":"https://pubmed.ncbi.nlm.nih.gov/19077267"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-531","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-531","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-531","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-531","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074570646","display_name":"Shashi Bhushan Pandit","orcid":"https://orcid.org/0000-0002-1362-5136"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shashi Bhushan Pandit","raw_affiliation_strings":["Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA. spandit3@mail.gatech.edu","Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA. spandit3@mail.gatech.edu","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010808261","display_name":"Jeffrey Skolnick","orcid":"https://orcid.org/0000-0002-1877-4958"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey Skolnick","raw_affiliation_strings":["Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.6677,"has_fulltext":true,"cited_by_count":142,"citation_normalized_percentile":{"value":0.9003681,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"9","issue":"1","first_page":"531","last_page":"531"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8307999968528748,"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":0.8307999968528748,"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":0.11100000143051147,"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/T10934","display_name":"Heat shock proteins research","score":0.008700000122189522,"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/structural-alignment","display_name":"Structural alignment","score":0.8430193662643433},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5871753692626953},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.557805061340332},{"id":"https://openalex.org/keywords/quality-score","display_name":"Quality Score","score":0.5134221315383911},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5104100108146667},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4877038896083832},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.44054752588272095},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.43160197138786316},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4132648706436157},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3871050477027893},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.36623597145080566},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.35128432512283325},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32688912749290466},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1796955168247223},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1780770719051361},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1296500563621521},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11536362767219543},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.08354228734970093}],"concepts":[{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.8430193662643433},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5871753692626953},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.557805061340332},{"id":"https://openalex.org/C2779346075","wikidata":"https://www.wikidata.org/wiki/Q7268763","display_name":"Quality Score","level":3,"score":0.5134221315383911},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5104100108146667},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4877038896083832},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.44054752588272095},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.43160197138786316},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4132648706436157},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3871050477027893},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.36623597145080566},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.35128432512283325},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32688912749290466},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1796955168247223},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1780770719051361},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1296500563621521},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11536362767219543},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.08354228734970093},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","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":"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":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"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},{"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":5,"locations":[{"id":"doi:10.1186/1471-2105-9-531","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-531","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-531","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19077267","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19077267","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:6d04da8346e248f5b312644d63211846","is_oa":false,"landing_page_url":"https://doaj.org/article/6d04da8346e248f5b312644d63211846","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Bioinformatics, Vol 9, Iss 1, p 531 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2628391","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2628391","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:smartech.gatech.edu:1853/27924","is_oa":true,"landing_page_url":"http://hdl.handle.net/1853/27924","pdf_url":null,"source":{"id":"https://openalex.org/S4377196313","display_name":"SMARTech Repository (Georgia Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I130701444","host_organization_name":"Georgia Institute of Technology","host_organization_lineage":["https://openalex.org/I130701444"],"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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-531","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-531","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-531","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2067852761.pdf","grobid_xml":"https://content.openalex.org/works/W2067852761.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1510161841","https://openalex.org/W1579228872","https://openalex.org/W1600613454","https://openalex.org/W1741740882","https://openalex.org/W1968002069","https://openalex.org/W1972718882","https://openalex.org/W1975453400","https://openalex.org/W1979147581","https://openalex.org/W1993279060","https://openalex.org/W2000468790","https://openalex.org/W2004667106","https://openalex.org/W2005049999","https://openalex.org/W2021953523","https://openalex.org/W2022058405","https://openalex.org/W2027853992","https://openalex.org/W2034100527","https://openalex.org/W2054849588","https://openalex.org/W2058987156","https://openalex.org/W2065283382","https://openalex.org/W2075610668","https://openalex.org/W2083440810","https://openalex.org/W2084367350","https://openalex.org/W2085277871","https://openalex.org/W2097311600","https://openalex.org/W2097642323","https://openalex.org/W2102245393","https://openalex.org/W2108067237","https://openalex.org/W2121125726","https://openalex.org/W2121702291","https://openalex.org/W2124241917","https://openalex.org/W2124358359","https://openalex.org/W2126016150","https://openalex.org/W2133225033","https://openalex.org/W2133715954","https://openalex.org/W2137146016","https://openalex.org/W2148101168","https://openalex.org/W2148376194","https://openalex.org/W2152326664","https://openalex.org/W2153193090","https://openalex.org/W2157938277","https://openalex.org/W2161151688","https://openalex.org/W2169870335","https://openalex.org/W2170471837","https://openalex.org/W3200464911","https://openalex.org/W4239426826","https://openalex.org/W4241510212"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W1482324242","https://openalex.org/W1985408726","https://openalex.org/W2088487249","https://openalex.org/W1870852322","https://openalex.org/W2107103206","https://openalex.org/W2414840205","https://openalex.org/W1741740882"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"tertiary":[2],"structure":[3,15,46,61,83,122],"comparisons":[4],"are":[5,135,144,273],"employed":[6],"in":[7,164,198,221,262],"various":[8,176],"fields":[9],"of":[10,20,39,64,74,111,157,271],"contemporary":[11],"structural":[12,34,103,159,191,208,260],"biology.":[13],"Most":[14],"comparison":[16,47,165,199,222,263],"methods":[17],"involve":[18],"generation":[19],"an":[21,230],"initial":[22,140,235],"seed":[23,141,236],"alignment,":[24],"which":[25],"is":[26,196,241],"extended":[27],"and/or":[28],"refined":[29,146],"to":[30,57,92,137,150,166,200,223,233,264],"provide":[31,58],"the":[32,52,65,79,81,99,125,139,152,155,158,190,207,239],"best":[33],"superposition":[35],"between":[36,71],"a":[37,45,59,72,109,214,249],"pair":[38,73],"protein":[40],"structures":[41,75],"as":[42,170,182],"assessed":[43],"by":[44,226],"metric.":[48],"One":[49],"such":[50,169,181],"metric,":[51],"TM-score,":[53,80],"was":[54,86,89,115],"recently":[55],"introduced":[56],"combined":[60],"quality":[62,161,178,193],"measure":[63],"coordinate":[66],"root":[67],"mean":[68],"square":[69],"deviation":[70],"and":[76,96,172,184,203,218,256,269],"coverage.":[77],"Using":[78],"TM-align":[82],"alignment":[84,104,123,160,177,192,255],"algorithm":[85,127,240,251],"developed":[87,130],"that":[88,143,189,252],"often":[90],"found":[91],"have":[93,213],"better":[94,197,259],"accuracy":[95],"coverage":[97,219],"than":[98,245],"most":[100],"commonly":[101],"used":[102,136],"programs;":[105],"however,":[106],"there":[107],"were":[108],"number":[110],"situations":[112],"when":[113],"this":[114],"not":[116],"true.":[117],"RESULTS:":[118],"To":[119],"further":[120],"improve":[121],"quality,":[124],"Fr-TM-align":[126,163,195,212,228,272],"has":[128],"been":[129],"where":[131],"aligned":[132],"fragment":[133,254],"pairs":[134],"generate":[138,234],"alignments":[142,209,261],"then":[145],"using":[147,211],"dynamic":[148],"programming":[149],"maximize":[151],"TM-score.":[153,185],"For":[154],"assessment":[156,179,187],"from":[162,194],"other":[167],"programs":[168],"CE":[171,202],"TM-align,":[173],"we":[174],"examined":[175],"scores":[180],"PSI":[183],"The":[186,266],"showed":[188],"both":[201],"TM-align.":[204,227,246,265],"On":[205],"average,":[206],"generated":[210,225],"higher":[215],"TM-score":[216],"(~9%)":[217],"(~7%)":[220],"those":[224],"uses":[229],"exhaustive":[231],"procedure":[232],"alignments.":[237],"Hence,":[238],"computationally":[242],"more":[243],"expensive":[244],"CONCLUSION:":[247],"Fr-TM-align,":[248],"new":[250],"employs":[253],"assembly":[257],"provides":[258],"source":[267],"code":[268],"executables":[270],"freely":[274],"downloadable":[275],"at:":[276],"http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.":[277]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":20},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":16}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}