{"id":"https://openalex.org/W2109362032","doi":"https://doi.org/10.1186/1471-2105-5-50","title":"A structural study for the optimisation of functional motifs encoded in protein sequences","display_name":"A structural study for the optimisation of functional motifs encoded in protein sequences","publication_year":2004,"publication_date":"2004-04-30","ids":{"openalex":"https://openalex.org/W2109362032","doi":"https://doi.org/10.1186/1471-2105-5-50","mag":"2109362032","pmid":"https://pubmed.ncbi.nlm.nih.gov/15119965"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-5-50","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-5-50","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-5-50","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/10.1186/1471-2105-5-50","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104561469","display_name":"Allegra Via","orcid":null},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Allegra Via","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Dept, of Biology, University of Rome Tor Vergata, Rome, Italy. allegra@cbm.bio.uniroma2.it","Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Dept, of Biology, University of Rome Tor Vergata, Rome, Italy. allegra@cbm.bio.uniroma2.it","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089562631","display_name":"Manuela Helmer\u2010Citterich","orcid":"https://orcid.org/0000-0001-9530-7504"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Manuela Helmer-Citterich","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, Rome (Italy)","Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, Rome (Italy)","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4824,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.62682623,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"5","issue":"1","first_page":"50","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3734000027179718,"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":0.3734000027179718,"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/T13526","display_name":"14-3-3 protein interactions","score":0.149399995803833,"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":0.035100001841783524,"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/false-positive-paradox","display_name":"False positive paradox","score":0.8296853303909302},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6315465569496155},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6073379516601562},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5876991152763367},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4833240509033203},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.48310065269470215},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4794958233833313},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.4763500988483429},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4241792559623718},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4112221598625183},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3692682385444641},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3422316312789917},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32065966725349426},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3025478422641754},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29398930072784424},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21402600407600403},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1525043547153473}],"concepts":[{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.8296853303909302},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6315465569496155},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6073379516601562},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5876991152763367},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4833240509033203},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.48310065269470215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4794958233833313},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4763500988483429},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4241792559623718},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4112221598625183},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3692682385444641},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3422316312789917},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32065966725349426},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3025478422641754},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29398930072784424},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21402600407600403},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1525043547153473},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005188","descriptor_name":"False Negative Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005188","descriptor_name":"False Negative Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005188","descriptor_name":"False Negative Reactions","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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-5-50","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-5-50","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-5-50","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:15119965","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15119965","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:art.torvergata.it:2108/14892","is_oa":true,"landing_page_url":"http://hdl.handle.net/2108/14892","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-5-50.pdf","source":{"id":"https://openalex.org/S4306400993","display_name":"Cineca Institutional Research Information System (Tor Vergata University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I116067653","host_organization_name":"University of Rome Tor Vergata","host_organization_lineage":["https://openalex.org/I116067653"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:0be6dded7db747168896013644e8f276","is_oa":false,"landing_page_url":"https://doaj.org/article/0be6dded7db747168896013644e8f276","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 5, Iss 1, p 50 (2004)","raw_type":"article"},{"id":"pmh:oai:iris.uniroma1.it:11573/395880","is_oa":false,"landing_page_url":"http://hdl.handle.net/11573/395880","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:420233","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/420233","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-5-50","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-5-50","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-5-50","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109362032.pdf","grobid_xml":"https://content.openalex.org/works/W2109362032.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W617763114","https://openalex.org/W1965907701","https://openalex.org/W1969051510","https://openalex.org/W1970654380","https://openalex.org/W1971143006","https://openalex.org/W1975998832","https://openalex.org/W1978526324","https://openalex.org/W1982996449","https://openalex.org/W1983655932","https://openalex.org/W1986969007","https://openalex.org/W1988599801","https://openalex.org/W1996423252","https://openalex.org/W2000468790","https://openalex.org/W2000629283","https://openalex.org/W2004994701","https://openalex.org/W2009566340","https://openalex.org/W2013843427","https://openalex.org/W2015642465","https://openalex.org/W2023790301","https://openalex.org/W2027045842","https://openalex.org/W2032991899","https://openalex.org/W2036667662","https://openalex.org/W2045119694","https://openalex.org/W2047544230","https://openalex.org/W2051895548","https://openalex.org/W2053803268","https://openalex.org/W2089173286","https://openalex.org/W2102431330","https://openalex.org/W2117019496","https://openalex.org/W2130479394","https://openalex.org/W2132094529","https://openalex.org/W2141885858","https://openalex.org/W2143173841","https://openalex.org/W2144333666","https://openalex.org/W2148853951","https://openalex.org/W2154333184","https://openalex.org/W2165979580","https://openalex.org/W2277690992","https://openalex.org/W4210531204"],"related_works":["https://openalex.org/W2181549235","https://openalex.org/W1973727281","https://openalex.org/W2046212479","https://openalex.org/W3209520725","https://openalex.org/W2003319012","https://openalex.org/W2031006065","https://openalex.org/W2514476306","https://openalex.org/W2023479323","https://openalex.org/W2143582965","https://openalex.org/W2044507120"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1],"large":[2],"number":[3],"of":[4,27,106,134,146,201,206,229,238,257,296,321,326],"PROSITE":[5,183,264],"patterns":[6,165,340],"select":[7,271],"false":[8],"positives":[9,126],"and/or":[10,25,41],"miss":[11],"known":[12],"true":[13,125,276,285],"positives.":[14],"It":[15],"is":[16,30,212,245,267,300,316],"possible":[17],"that--at":[18],"least":[19,283],"in":[20,48,66,74,85,120,191,219,329],"some":[21,220,228],"cases--the":[22],"weak":[23],"specificity":[24,105],"sensitivity":[26,102,174,224],"a":[28,69,75,86,95,128,135,330],"pattern":[29,88,154,198,216,261,322],"due":[31],"to":[32,57,82,157,181,196,214,254,270],"the":[33,49,101,143,147,153,163,169,192,197,204,230,233,236,275,294,319],"fact":[34],"that":[35,123],"one,":[36],"or":[37,104,260,338],"maybe":[38],"more,":[39],"functional":[40,59,258],"structural":[42,210],"key":[43],"residues":[44,63,117,150,188,299],"are":[45,54,80,124,130,155,166,189,288,341],"not":[46,268],"represented":[47],"pattern.":[50],"Multiple":[51],"sequence":[52,60,77,144,160],"alignments":[53],"commonly":[55],"used":[56,156],"build":[58,158],"patterns.":[61,108,161,184],"If":[62],"structurally":[64,118,148,186,297],"conserved":[65,119,149,187,298],"proteins":[67],"sharing":[68],"function":[70],"cannot":[71],"be":[72,83,112,252,307],"aligned":[73],"multiple":[76],"alignment,":[78],"they":[79],"likely":[81],"missed":[84],"standard":[87],"construction":[89],"procedure.":[90],"RESULTS:":[91],"Here":[92],"we":[93],"present":[94],"new":[96],"procedure":[97,110,234,315],"aimed":[98],"at":[99,282],"improving":[100],"and/":[103],"poorly-performing":[107],"The":[109,177,290,314],"can":[111,251],"summarised":[113],"as":[114,225],"follows:":[115],"1.":[116],"different":[121],"proteins,":[122],"for":[127,172,280,293,318,334],"pattern,":[129],"identified":[131],"by":[132,139],"means":[133],"computational":[136,291],"technique":[137,292],"and":[138,175,218,223,273,279,305,325],"visual":[140],"inspection.":[141],"2.":[142],"positions":[145],"falling":[151],"outside":[152],"extended":[159,164],"3.":[162],"optimised":[167],"on":[168,303,310],"SWISS-PROT":[170],"database":[171,323],"their":[173],"specificity.":[176],"method":[178,250],"was":[179],"applied":[180,253],"eight":[182,202],"Whenever":[185],"found":[190],"surface":[193],"region":[194],"close":[195],"(seven":[199],"out":[200],"cases),":[203],"addition":[205],"information":[207],"inferred":[208],"from":[209],"analysis":[211],"shown":[213],"improve":[215],"selectivity":[217,222],"cases":[221,231],"well.":[226],"In":[227],"considered":[232],"allowed":[235],"identification":[237,295],"functionally":[239],"interesting":[240],"residues,":[241],"whose":[242],"biological":[243],"role":[244],"also":[246],"discussed.":[247],"CONCLUSION:":[248],"Our":[249],"any":[255],"type":[256],"motif":[259],"(not":[262],"only":[263,274],"ones)":[265],"which":[266,281,335],"able":[269],"all":[272],"positive":[277,286],"hits":[278],"two":[284],"structures":[287],"available.":[289,343],"already":[301],"available":[302],"request":[304],"will":[306],"soon":[308],"accessible":[309],"our":[311],"web":[312],"server.":[313],"intended":[317],"use":[320],"curators":[324],"scientists":[327],"interested":[328],"specific":[331,337],"protein":[332],"family":[333],"no":[336],"selective":[339],"yet":[342]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-18T10:00:31.954636","created_date":"2025-10-10T00:00:00"}