{"id":"https://openalex.org/W2101058639","doi":"https://doi.org/10.1186/1471-2105-12-226","title":"StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase","display_name":"StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase","publication_year":2011,"publication_date":"2011-06-02","ids":{"openalex":"https://openalex.org/W2101058639","doi":"https://doi.org/10.1186/1471-2105-12-226","mag":"2101058639","pmid":"https://pubmed.ncbi.nlm.nih.gov/21635786"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-226","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-226","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-226","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/10.1186/1471-2105-12-226","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083445132","display_name":"Adam Zem\u0142a","orcid":"https://orcid.org/0000-0003-0504-8647"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam T Zemla","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. zemla1@llnl.gov","Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA. zemla1@llnl.gov","institution_ids":["https://openalex.org/I4210138311"]},{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040343543","display_name":"Dorothy Lang","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dorothy M Lang","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA","Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]},{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034839753","display_name":"Tanya Kostova","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I1311060795","display_name":"U.S. National Science Foundation","ror":"https://ror.org/021nxhr62","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tanya Kostova","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA","[National Science Foundation, Arlington, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]},{"raw_affiliation_string":"[National Science Foundation, Arlington, USA]","institution_ids":["https://openalex.org/I1311060795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006463024","display_name":"Raul Andino","orcid":"https://orcid.org/0000-0001-5503-9349"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raul Andino","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA","Department of Microbiology & Immunology, University of California San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]},{"raw_affiliation_string":"Department of Microbiology & Immunology, University of California San Francisco, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113814626","display_name":"Carol Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carol L Ecale Zhou","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, USA","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"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":0.7984,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.71735295,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"226","last_page":"226"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6294000148773193,"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":0.6294000148773193,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.18299999833106995,"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":0.02669999934732914,"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":0.7024973630905151},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6769182085990906},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6416471600532532},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5547785758972168},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5459545850753784},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.5056941509246826},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4698333442211151},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4182504117488861},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4124656915664673},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4020007252693176},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3965708315372467},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.31704121828079224},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1626100242137909},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.162203848361969},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11517629027366638}],"concepts":[{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.7024973630905151},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6769182085990906},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6416471600532532},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5547785758972168},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5459545850753784},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.5056941509246826},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4698333442211151},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4182504117488861},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4124656915664673},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4020007252693176},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3965708315372467},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.31704121828079224},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1626100242137909},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.162203848361969},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11517629027366638}],"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012324","descriptor_name":"RNA-Dependent RNA Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017955","descriptor_name":"Poliovirus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D017955","descriptor_name":"Poliovirus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D017955","descriptor_name":"Poliovirus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D017955","descriptor_name":"Poliovirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017955","descriptor_name":"Poliovirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017955","descriptor_name":"Poliovirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-12-226","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-226","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-226","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:21635786","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21635786","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:info:ark/67531/metadc840242","is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc840242/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Name: BMC Bioinformatics; Journal Volume: 12","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:733eda023ae44cb28a99329012be1fe6","is_oa":false,"landing_page_url":"https://doaj.org/article/733eda023ae44cb28a99329012be1fe6","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 12, Iss 1, p 226 (2011)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1027977","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1027977","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1626277","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626277","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3121648","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3121648","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-226","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-226","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-226","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G4343739756","display_name":null,"funder_award_id":"Contract DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G4844777956","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320337547","funder_display_name":"Laboratory Directed Research and Development"},{"id":"https://openalex.org/G5522089832","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G5816449448","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G69709960","display_name":null,"funder_award_id":"Contract DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7806955302","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8374966015","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G991281326","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101058639.pdf","grobid_xml":"https://content.openalex.org/works/W2101058639.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1622733315","https://openalex.org/W1762168883","https://openalex.org/W1793294936","https://openalex.org/W1801992990","https://openalex.org/W1812972501","https://openalex.org/W1932632320","https://openalex.org/W1967154222","https://openalex.org/W1967439544","https://openalex.org/W1967538863","https://openalex.org/W1984197379","https://openalex.org/W1994278598","https://openalex.org/W2000377676","https://openalex.org/W2008708467","https://openalex.org/W2021677726","https://openalex.org/W2031926002","https://openalex.org/W2037695366","https://openalex.org/W2040837844","https://openalex.org/W2053281575","https://openalex.org/W2054896136","https://openalex.org/W2055140930","https://openalex.org/W2085277871","https://openalex.org/W2085323444","https://openalex.org/W2087151779","https://openalex.org/W2095425492","https://openalex.org/W2097642323","https://openalex.org/W2101220662","https://openalex.org/W2109174354","https://openalex.org/W2109851929","https://openalex.org/W2110483430","https://openalex.org/W2110670926","https://openalex.org/W2111586169","https://openalex.org/W2117717845","https://openalex.org/W2118848130","https://openalex.org/W2123070828","https://openalex.org/W2126048802","https://openalex.org/W2127868702","https://openalex.org/W2141805605","https://openalex.org/W2169558621","https://openalex.org/W4252178616"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2029514038","https://openalex.org/W2111937814","https://openalex.org/W2133116680","https://openalex.org/W1482324242","https://openalex.org/W2141411672","https://openalex.org/W2468116983","https://openalex.org/W2088487249","https://openalex.org/W187239587","https://openalex.org/W2158700816"],"abstract_inverted_index":{"BACKGROUND:":[0],"Most":[1],"of":[2,31,54,78,102,146,151,165,206,273],"the":[3,42,52,58,84,100,147,157,166],"currently":[4],"used":[5,161,262],"methods":[6,66],"for":[7,21,35,125,245],"protein":[8,18,112,167],"function":[9],"prediction":[10],"rely":[11],"on":[12],"sequence-based":[13],"comparisons":[14],"between":[15,57,110],"a":[16,23,122,144,220,241,255,287,295],"query":[17],"and":[19,131,153,229,247,267],"those":[20],"which":[22],"functional":[24,204,277],"annotation":[25],"is":[26,41,61,240,292],"provided.":[27],"A":[28],"serious":[29],"limitation":[30],"sequence":[32,55,64,79,120,289],"similarity-based":[33],"approaches":[34],"identifying":[36,246],"residue":[37,133,187],"conservation":[38],"among":[39,49,189],"proteins":[40,50,60,178],"low":[43,76],"confidence":[44],"in":[45,83,143],"assigning":[46],"residue-residue":[47,108,191,265],"correspondences":[48,109,266],"when":[51],"level":[53],"identity":[56],"compared":[59,111],"poor.":[62],"Multiple":[63],"alignment":[65],"are":[67,169,210],"more":[68],"satisfactory--still,":[69],"they":[70],"cannot":[71],"provide":[72],"reliable":[73],"results":[74],"at":[75,286,298],"levels":[77],"identity.":[80],"Our":[81],"goal":[82],"current":[85],"work":[86],"was":[87],"to":[88,162,212,254,263],"develop":[89],"an":[90],"algorithm":[91,124,158,244],"that":[92,156,168,173,179,209,217,225,251,270],"could":[93],"help":[94],"overcome":[95],"these":[96],"difficulties":[97],"by":[98],"facilitating":[99],"identification":[101],"structurally":[103],"(and":[104],"possibly":[105],"functionally)":[106],"relevant":[107],"structures.":[113],"RESULTS:":[114],"Here":[115],"we":[116,154],"present":[117],"StralSV":[118,142,236,239,258,291],"(structure-alignment":[119],"variability),":[121],"new":[123,242],"detecting":[126],"closely":[127],"related":[128],"structure":[129,138,249],"fragments":[130,250],"quantifying":[132,186],"frequency":[134],"from":[135,194,219,235],"tight":[136],"local":[137,195],"alignments.":[139],"We":[140,222],"apply":[141],"study":[145],"RNA-dependent":[148],"RNA":[149],"polymerase":[150],"poliovirus,":[152],"demonstrate":[155,224],"can":[159,199,232,260],"be":[160,181,213,233,261,272],"determine":[163],"regions":[164],"relatively":[170],"unique,":[171],"or":[172,203,216,276,283],"share":[174],"structural":[175,196,202,228,275],"similarity":[176,253],"with":[177],"would":[180],"considered":[182],"distantly":[183],"related.":[184],"By":[185],"frequencies":[188],"many":[190],"pairs":[192],"extracted":[193],"alignments,":[197],"one":[198],"infer":[200],"potential":[201],"importance":[205],"specific":[207],"residues":[208,269,285],"determined":[211],"highly":[214],"conserved":[215],"deviate":[218],"consensus.":[221],"further":[223],"considerable":[226],"detailed":[227],"phylogenetic":[230],"information":[231],"derived":[234],"analyses.":[237],"CONCLUSIONS:":[238],"structure-based":[243],"aligning":[248],"have":[252],"reference":[256],"protein.":[257],"analysis":[259],"quantify":[264],"identify":[268],"may":[271],"particular":[274],"importance,":[278],"as":[279,281,294],"well":[280],"unusual":[282],"unexpected":[284],"given":[288],"position.":[290],"provided":[293],"web":[296],"service":[297],"http://proteinmodel.org/AS2TS/STRALSV/.":[299]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}