{"id":"https://openalex.org/W2156914590","doi":"https://doi.org/10.1093/bioinformatics/btm262","title":"An evaluation of automated homology modelling methods at low target\u2013template sequence similarity","display_name":"An evaluation of automated homology modelling methods at low target\u2013template sequence similarity","publication_year":2007,"publication_date":"2007-05-17","ids":{"openalex":"https://openalex.org/W2156914590","doi":"https://doi.org/10.1093/bioinformatics/btm262","mag":"2156914590","pmid":"https://pubmed.ncbi.nlm.nih.gov/17510171"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm262","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm262","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/15/1901/49814516/bioinformatics_23_15_1901.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/23/15/1901/49814516/bioinformatics_23_15_1901.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007039649","display_name":"James A. R. Dalton","orcid":"https://orcid.org/0000-0002-5279-4581"},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"James A. R. Dalton","raw_affiliation_strings":["Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK","institution_ids":["https://openalex.org/I130828816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015550435","display_name":"Richard M. Jackson","orcid":null},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard M. Jackson","raw_affiliation_strings":["Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK","institution_ids":["https://openalex.org/I130828816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5007039649"],"corresponding_institution_ids":["https://openalex.org/I130828816"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.4031,"has_fulltext":true,"cited_by_count":97,"citation_normalized_percentile":{"value":0.93241697,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"23","issue":"15","first_page":"1901","last_page":"1908"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.995199978351593,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9941999912261963,"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/computer-science","display_name":"Computer science","score":0.6266522407531738},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5586893558502197},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5013008117675781},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4914819002151489},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.45394614338874817},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44399285316467285},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.41373714804649353},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4132160544395447},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40554946660995483},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2012331783771515},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.18902790546417236},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12892025709152222},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1247728168964386},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07460403442382812}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6266522407531738},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5586893558502197},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5013008117675781},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4914819002151489},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.45394614338874817},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44399285316467285},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.41373714804649353},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4132160544395447},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40554946660995483},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2012331783771515},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.18902790546417236},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12892025709152222},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1247728168964386},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07460403442382812},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"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/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm262","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm262","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/15/1901/49814516/bioinformatics_23_15_1901.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:17510171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17510171","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm262","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm262","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/15/1901/49814516/bioinformatics_23_15_1901.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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2156914590.pdf","grobid_xml":"https://content.openalex.org/works/W2156914590.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W53898165","https://openalex.org/W1508885706","https://openalex.org/W1964457244","https://openalex.org/W1967935580","https://openalex.org/W1970197953","https://openalex.org/W1977689937","https://openalex.org/W1979147581","https://openalex.org/W1980374511","https://openalex.org/W1981207136","https://openalex.org/W1985408726","https://openalex.org/W2004228538","https://openalex.org/W2012046786","https://openalex.org/W2047163848","https://openalex.org/W2055043387","https://openalex.org/W2060809301","https://openalex.org/W2065283382","https://openalex.org/W2073758233","https://openalex.org/W2077529366","https://openalex.org/W2080948893","https://openalex.org/W2085277871","https://openalex.org/W2103273582","https://openalex.org/W2107103206","https://openalex.org/W2108138353","https://openalex.org/W2115451817","https://openalex.org/W2127122014","https://openalex.org/W2127658176","https://openalex.org/W2143292980","https://openalex.org/W2149007706","https://openalex.org/W2149480059","https://openalex.org/W2152326664","https://openalex.org/W2156469184","https://openalex.org/W2158307923","https://openalex.org/W4241855343","https://openalex.org/W6602161028"],"related_works":["https://openalex.org/W2375480909","https://openalex.org/W2353314428","https://openalex.org/W3130075881","https://openalex.org/W2059079931","https://openalex.org/W2157930580","https://openalex.org/W3093039011","https://openalex.org/W2762504776","https://openalex.org/W3045302716","https://openalex.org/W1595347157","https://openalex.org/W2406523068"],"abstract_inverted_index":{"When":[0],"using":[1,13,36,44],"Modeller":[2,98],"as":[3,82],"the":[4,18,24,91,106,114,126],"common":[5],"modelling":[6,62,94,104],"program,":[7],"3D-Coffee":[8,35,59],"outperforms":[9],"Staccato":[10,55,70],"and":[11,17,22,41,48,56,66,71],"SAlign":[12,72],"both":[14],"multiple":[15,37,65],"templates":[16,38,87],"best":[19,115],"single":[20,45,67,77],"template,":[21],"across":[23],"sequence":[25,85],"identity":[26,86],"range":[27],"20-50%.":[28],"The":[29],"mean":[30,122],"model":[31],"RMSD":[32,123],"generated":[33,53,128],"from":[34,64],"is":[39],"15":[40],"28%":[42],"(or":[43],"templates,":[46,68,78],"3":[47],"13%)":[49],"better":[50,101],"than":[51,105],"those":[52],"by":[54,121,129],"Salign,":[57],"respectively.":[58],"gives":[60],"equivalent":[61],"accuracy":[63],"but":[69],"are":[73,88],"more":[74],"successful":[75],"with":[76,117],"their":[79],"quality":[80],"deteriorating":[81],"additional":[83],"lower":[84],"added.":[89],"Evaluating":[90],"different":[92],"homology":[93],"programs,":[95],"on":[96,110],"average":[97,111],"performs":[99],"marginally":[100],"in":[102],"overall":[103],"others":[107],"tested.":[108],"However,":[109],"Nest":[112],"produces":[113],"loops":[116,127],"an":[118],"8%":[119],"improvement":[120],"compared":[124],"to":[125],"Builder.":[130]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
