{"id":"https://openalex.org/W2007978853","doi":"https://doi.org/10.1186/1471-2105-9-17","title":"Prediction of enzyme function based on 3D templates of evolutionarily important amino acids","display_name":"Prediction of enzyme function based on 3D templates of evolutionarily important amino acids","publication_year":2008,"publication_date":"2008-01-11","ids":{"openalex":"https://openalex.org/W2007978853","doi":"https://doi.org/10.1186/1471-2105-9-17","mag":"2007978853","pmid":"https://pubmed.ncbi.nlm.nih.gov/18190718"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-17","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-17","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-17","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042113315","display_name":"David M. Kristensen","orcid":"https://orcid.org/0000-0003-0657-1632"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210162370","display_name":"Baylor Genetics","ror":"https://ror.org/05bxjx840","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210162370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David M Kristensen","raw_affiliation_strings":["Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. dk131363@gmail.com","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. dk131363@gmail.com","institution_ids":["https://openalex.org/I181547552","https://openalex.org/I4210162370"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044814535","display_name":"R. Matthew Ward","orcid":null},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R Matthew Ward","raw_affiliation_strings":["Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076793372","display_name":"Andreas Martin Lisewski","orcid":"https://orcid.org/0000-0003-3403-6880"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Martin Lisewski","raw_affiliation_strings":["Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083076717","display_name":"Serkan Erdin","orcid":"https://orcid.org/0000-0001-6587-2625"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Serkan Erdin","raw_affiliation_strings":["Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062182398","display_name":"Brian Y. Chen","orcid":"https://orcid.org/0000-0001-9025-0107"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Y Chen","raw_affiliation_strings":["Department of Computer Science, Rice University, Houston, Texas, 77030, USA","Department of Computer Science, Rice University, Houston, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, Texas, 77030, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, USA#TAB#","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035723276","display_name":"Viacheslav Y. Fofanov","orcid":"https://orcid.org/0000-0001-7142-0764"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Viacheslav Y Fofanov","raw_affiliation_strings":["Department of Statistics, Rice University, Houston, Texas, 77030, USA","Department of Statistics Rice University Houston USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, Texas, 77030, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Statistics Rice University Houston USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071222148","display_name":"Marek Kimmel","orcid":"https://orcid.org/0000-0001-8161-890X"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marek Kimmel","raw_affiliation_strings":["Department of Statistics, Rice University, Houston, Texas, 77030, USA","Department of Statistics Rice University Houston USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, Texas, 77030, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Statistics Rice University Houston USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lydia E Kavraki","raw_affiliation_strings":["Department of Bioengineering, Rice University, Houston, Texas, 77030, USA","Department of Computer Science, Rice University, Houston, Texas, 77030, USA","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Department of Computer Science, Rice University, Houston, USA","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Rice University, Houston, Texas, 77030, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, Texas, 77030, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, Houston, USA","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023680746","display_name":"Olivier Lichtarge","orcid":"https://orcid.org/0000-0003-4057-7122"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Olivier Lichtarge","raw_affiliation_strings":["Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, USA","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023680746"],"corresponding_institution_ids":["https://openalex.org/I181547552"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":5.31,"has_fulltext":true,"cited_by_count":75,"citation_normalized_percentile":{"value":0.96452698,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5515000224113464,"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":0.5515000224113464,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.13750000298023224,"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":0.10270000249147415,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.7725163698196411},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.6023638248443604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5733709335327148},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5540600419044495},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5221662521362305},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.46041256189346313},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4075629711151123},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38710030913352966},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.332613080739975},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13622447848320007},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09669792652130127},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07559344172477722}],"concepts":[{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.7725163698196411},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6023638248443604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5733709335327148},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5540600419044495},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5221662521362305},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.46041256189346313},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4075629711151123},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38710030913352966},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.332613080739975},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13622447848320007},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09669792652130127},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07559344172477722}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","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":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-9-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-17","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-17","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18190718","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18190718","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:1832176","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2219985","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":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b3d726a02feb4d6fae48760435f2c4ad","is_oa":false,"landing_page_url":"https://doaj.org/article/b3d726a02feb4d6fae48760435f2c4ad","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 17 (2008)","raw_type":"article"},{"id":"doi:10.7916/d8nc5zp5","is_oa":true,"landing_page_url":"https://doi.org/10.7916/d8nc5zp5","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-17","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-17","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-17","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1119704899","display_name":"Automated Annotation of Function in Protein Structures from Evolutionary-based 3D-Templates","funder_award_id":"0547695","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2147181636","display_name":null,"funder_award_id":"R01GM079656","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G215298234","display_name":"Medical Genetics Research Fellowship Program","funder_award_id":"2t32gm007526-46","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2246459070","display_name":"Vertical Integration of Research and Education in the Mathematical Sciences","funder_award_id":"0240058","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2640905883","display_name":null,"funder_award_id":"T15LM007093","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G2721229416","display_name":null,"funder_award_id":"5 T32 GM07526-29","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3142106742","display_name":null,"funder_award_id":"NIH 5 T32","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G44224349","display_name":"Functional Determinants in G-Protein-Coupled Receptors","funder_award_id":"5r01gm066099-17","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4797008958","display_name":null,"funder_award_id":"R01-GM066099","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5338120705","display_name":"Comparative genomics of protein structure and function","funder_award_id":"5r01gm079656-12","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G547321803","display_name":null,"funder_award_id":"T32GM007526","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G64683279","display_name":null,"funder_award_id":"5T15-LM-07093","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G709425730","display_name":null,"funder_award_id":"GM066099","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G846939263","display_name":null,"funder_award_id":"GM-079656","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"},{"id":"https://openalex.org/F4320306182","display_name":"March of Dimes Foundation","ror":"https://ror.org/04bd5p711"},{"id":"https://openalex.org/F4320310133","display_name":"Rice University","ror":"https://ror.org/008zs3103"},{"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"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2007978853.pdf","grobid_xml":"https://content.openalex.org/works/W2007978853.grobid-xml"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W1509280691","https://openalex.org/W1570722626","https://openalex.org/W1580328099","https://openalex.org/W1582255757","https://openalex.org/W1614421135","https://openalex.org/W1964640688","https://openalex.org/W1978462051","https://openalex.org/W1983747555","https://openalex.org/W1986969007","https://openalex.org/W1992115216","https://openalex.org/W1993267991","https://openalex.org/W1999319994","https://openalex.org/W2003788979","https://openalex.org/W2007872355","https://openalex.org/W2008708467","https://openalex.org/W2021954541","https://openalex.org/W2022058405","https://openalex.org/W2032838501","https://openalex.org/W2043199972","https://openalex.org/W2046977075","https://openalex.org/W2050330741","https://openalex.org/W2053803268","https://openalex.org/W2055043387","https://openalex.org/W2059345747","https://openalex.org/W2063982943","https://openalex.org/W2067364375","https://openalex.org/W2085277871","https://openalex.org/W2088534163","https://openalex.org/W2089922354","https://openalex.org/W2091563009","https://openalex.org/W2096039340","https://openalex.org/W2097108043","https://openalex.org/W2098223336","https://openalex.org/W2100320834","https://openalex.org/W2100494857","https://openalex.org/W2102333330","https://openalex.org/W2102612168","https://openalex.org/W2103017472","https://openalex.org/W2103150692","https://openalex.org/W2103794058","https://openalex.org/W2107327414","https://openalex.org/W2108302275","https://openalex.org/W2110591305","https://openalex.org/W2114520383","https://openalex.org/W2115230913","https://openalex.org/W2117164735","https://openalex.org/W2123858481","https://openalex.org/W2124410686","https://openalex.org/W2124815061","https://openalex.org/W2127056957","https://openalex.org/W2127648442","https://openalex.org/W2128996066","https://openalex.org/W2129046747","https://openalex.org/W2130479394","https://openalex.org/W2133225033","https://openalex.org/W2133990057","https://openalex.org/W2137071423","https://openalex.org/W2137503746","https://openalex.org/W2137991504","https://openalex.org/W2137995988","https://openalex.org/W2144998676","https://openalex.org/W2146939455","https://openalex.org/W2146940292","https://openalex.org/W2153463820","https://openalex.org/W2156728093","https://openalex.org/W2158714788","https://openalex.org/W2161938295","https://openalex.org/W2162574056","https://openalex.org/W2165979580","https://openalex.org/W2166278492","https://openalex.org/W2168211076","https://openalex.org/W2170471837","https://openalex.org/W2171172158","https://openalex.org/W4205241946","https://openalex.org/W4236463195","https://openalex.org/W4285719527","https://openalex.org/W6600882715"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W4234406076","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W2010731026","https://openalex.org/W2360893094","https://openalex.org/W4390787808","https://openalex.org/W4236036386","https://openalex.org/W4231091074"],"abstract_inverted_index":{"BACKGROUND:":[0],"Structural":[1],"genomics":[2],"projects":[3],"such":[4,165],"as":[5,136,154],"the":[6,108,130,137,155,158,170,195,208,219,254,258,264,287],"Protein":[7],"Structure":[8],"Initiative":[9],"(PSI)":[10],"yield":[11],"many":[12,143],"new":[13],"structures,":[14],"but":[15],"often":[16],"these":[17,163],"have":[18],"no":[19],"known":[20],"molecular":[21],"functions.":[22],"One":[23],"approach":[24],"to":[25,30,54,66,80,180,183,191,199,277,282],"recover":[26],"this":[27,74],"information":[28,91],"is":[29,211],"use":[31],"3D":[32,68,85,196,251],"templates":[33,69,101],"-":[34],"structure-function":[35],"motifs":[36],"that":[37,235],"consist":[38],"of":[39,126,140,221,237,263],"a":[40,71,77,114,146,166,270],"few":[41],"functionally":[42],"critical":[43],"amino":[44],"acids":[45],"and":[46,92,110,161,198,274],"may":[47],"suggest":[48,234],"functional":[49,60,242],"similarity":[50],"when":[51],"geometrically":[52,193],"matched":[53,122],"other":[55,250,280],"structures.":[56],"Since":[57],"experimentally":[58],"determined":[59],"sites":[61],"are":[62,189,228],"not":[63],"common":[64],"enough":[65],"define":[67],"on":[70,89],"large":[72,272],"scale,":[73,273],"work":[75],"tests":[76],"computational":[78],"strategy":[79],"select":[81],"relevant":[82],"residues":[83,240],"for":[84,102,260],"templates.":[86],"RESULTS:":[87],"Based":[88],"evolutionary":[90],"heuristics,":[93],"an":[94],"Evolutionary":[95],"Trace":[96],"Annotation":[97],"(ETA)":[98],"pipeline":[99],"built":[100],"98":[103],"enzymes,":[104],"half":[105],"taken":[106],"from":[107],"PSI,":[109],"sought":[111],"matches":[112,188],"in":[113,162,218,286],"non-redundant":[115],"structure":[116],"database.":[117],"On":[118],"average":[119],"each":[120],"template":[121,197,252],"2.7":[123],"distinct":[124],"proteins,":[125],"which":[127],"2.0":[128],"share":[129],"first":[131],"three":[132],"Enzyme":[133],"Commission":[134],"digits":[135],"template's":[138],"enzyme":[139,246],"origin.":[141],"In":[142],"cases":[144,164],"(61%)":[145],"single":[147],"most":[148,159],"likely":[149],"function":[150,172,285],"could":[151],"be":[152,181,200],"predicted":[153],"annotation":[156,209,243],"with":[157,173,279],"matches,":[160],"plurality":[167],"vote":[168],"identified":[169],"correct":[171],"87%":[174],"accuracy.":[175],"ETA":[176,255],"was":[177],"also":[178],"found":[179,203],"complementary":[182],"sequence":[184,201,223],"homology-based":[185,226],"annotations.":[186],"When":[187],"required":[190],"both":[192],"match":[194],"homologs":[202],"by":[204],"BLAST":[205],"or":[206],"PSI-BLAST,":[207],"accuracy":[210],"greater":[212],"than":[213],"either":[214],"method":[215,256],"alone,":[216],"especially":[217],"region":[220],"lower":[222],"identity":[224],"where":[225],"annotations":[227],"least":[229],"reliable.":[230],"CONCLUSION:":[231],"These":[232],"data":[233],"knowledge":[236,262],"evolutionarily":[238],"important":[239],"improves":[241],"among":[244],"distant":[245],"homologs.":[247],"Since,":[248],"unlike":[249],"approaches,":[253],"bypasses":[257],"need":[259],"experimental":[261],"catalytic":[265],"mechanism,":[266],"it":[267],"should":[268],"prove":[269],"useful,":[271],"general":[275],"adjunct":[276],"combine":[278],"methods":[281],"decipher":[283],"protein":[284],"structural":[288],"proteome.":[289]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":8}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}