{"id":"https://openalex.org/W2105788709","doi":"https://doi.org/10.1093/bioinformatics/btm524","title":"A computational strategy for the prediction of functional linear peptide motifs in proteins","display_name":"A computational strategy for the prediction of functional linear peptide motifs in proteins","publication_year":2007,"publication_date":"2007-10-31","ids":{"openalex":"https://openalex.org/W2105788709","doi":"https://doi.org/10.1093/bioinformatics/btm524","mag":"2105788709","pmid":"https://pubmed.ncbi.nlm.nih.gov/17977881"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm524","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm524","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/24/3297/16861906/btm524.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/23/24/3297/16861906/btm524.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073222103","display_name":"Holger Dinkel","orcid":"https://orcid.org/0000-0002-9316-5204"},"institutions":[{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Holger Dinkel","raw_affiliation_strings":["Abteilung f\u00fcr Bioinformatik, Institut f\u00fcr Biochemie, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg, 91054 Erlangen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Abteilung f\u00fcr Bioinformatik, Institut f\u00fcr Biochemie, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg, 91054 Erlangen, Germany","institution_ids":["https://openalex.org/I181369854"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065393453","display_name":"Heinrich Sticht","orcid":"https://orcid.org/0000-0001-5644-045X"},"institutions":[{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Heinrich Sticht","raw_affiliation_strings":["Abteilung f\u00fcr Bioinformatik, Institut f\u00fcr Biochemie, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg, 91054 Erlangen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Abteilung f\u00fcr Bioinformatik, Institut f\u00fcr Biochemie, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg, 91054 Erlangen, Germany","institution_ids":["https://openalex.org/I181369854"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5065393453"],"corresponding_institution_ids":["https://openalex.org/I181369854"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.1318,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.87152857,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"23","issue":"24","first_page":"3297","last_page":"3303"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9994000196456909,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9994000196456909,"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":0.9991999864578247,"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":0.9991999864578247,"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/sequence","display_name":"Sequence (biology)","score":0.6268929243087769},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6236943006515503},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5664293766021729},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5348104238510132},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5156668424606323},{"id":"https://openalex.org/keywords/sequence-logo","display_name":"Sequence logo","score":0.4955383539199829},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.4478078782558441},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.43248656392097473},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.37873348593711853},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3286331593990326},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2962644100189209},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2718072533607483},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14906153082847595}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6268929243087769},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6236943006515503},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5664293766021729},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5348104238510132},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5156668424606323},{"id":"https://openalex.org/C105082737","wikidata":"https://www.wikidata.org/wiki/Q7452470","display_name":"Sequence logo","level":5,"score":0.4955383539199829},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.4478078782558441},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.43248656392097473},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.37873348593711853},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3286331593990326},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2962644100189209},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2718072533607483},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14906153082847595},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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},{"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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm524","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm524","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/24/3297/16861906/btm524.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:17977881","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17977881","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},{"id":"pmh:oai:pure.mpg.de:item_3283076","is_oa":false,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0007-E2D3-B","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm524","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm524","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/24/3297/16861906/btm524.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":[{"score":0.6399999856948853,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1971147414","https://openalex.org/W1982481323","https://openalex.org/W2008841836","https://openalex.org/W2036511353","https://openalex.org/W2041449172","https://openalex.org/W2052033556","https://openalex.org/W2055043387","https://openalex.org/W2062296203","https://openalex.org/W2078381702","https://openalex.org/W2085037886","https://openalex.org/W2102956364","https://openalex.org/W2129448726","https://openalex.org/W2131224722","https://openalex.org/W2152770371","https://openalex.org/W2153250803","https://openalex.org/W2154412571","https://openalex.org/W2161732286","https://openalex.org/W2168514491"],"related_works":["https://openalex.org/W2036521446","https://openalex.org/W2019019284","https://openalex.org/W1727089480","https://openalex.org/W3149778688","https://openalex.org/W2164809504","https://openalex.org/W2914535664","https://openalex.org/W2183608621","https://openalex.org/W2133328876","https://openalex.org/W2208708370","https://openalex.org/W2087687984"],"abstract_inverted_index":{"MOTIVATION:":[0],"Short":[1],"linear":[2,104,205],"peptide":[3,206],"motifs":[4,22,36,122,162,207],"mediate":[5],"protein-protein":[6],"interaction,":[7],"cell":[8],"compartment":[9],"targeting":[10],"and":[11,149],"represent":[12],"the":[13,31,35,59,76,80,143,150,164,182],"sites":[14],"of":[15,20,34,42,44,61,87,108,126,133,146,159,181],"post-translational":[16],"modification.":[17],"The":[18,106],"identification":[19,60],"functional":[21,62,161,183],"by":[23,30,71,113],"conventional":[24],"sequence":[25,77,90,98,147],"searches,":[26],"however,":[27],"is":[28,50],"hampered":[29],"short":[32,204],"length":[33],"resulting":[37],"in":[38,68,130,155,185],"a":[39,47,56,84,124,131,139,156,210],"large":[40],"number":[41],"hits":[43,173],"which":[45,64],"only":[46,169],"small":[48],"portion":[49],"functional.":[51,215],"RESULTS:":[52],"We":[53],"have":[54,92,209],"developed":[55],"procedure":[57],"for":[58],"motifs,":[63],"scores":[65],"pattern":[66],"conservation":[67],"homologous":[69],"sequences":[70],"taking":[72],"explicitly":[73],"into":[74],"account":[75],"similarity":[78],"to":[79,95,117,138,175,178,195,213],"query":[81],"sequence.":[82],"For":[83],"further":[85],"improvement":[86],"this":[88,109,189],"method,":[89],"filters":[91,148],"been":[93],"optimized":[94],"mask":[96],"those":[97,203],"regions":[99],"containing":[100],"little":[101],"or":[102],"no":[103],"motifs.":[105],"performance":[107],"approach":[110,191],"was":[111],"verified":[112],"measuring":[114],"its":[115],"ability":[116],"identify":[118],"576":[119],"experimentally":[120],"validated":[121,160],"among":[123],"total":[125],"15":[127],"563":[128],"instances":[129,184],"set":[132],"415":[134],"protein":[135],"sequences.":[136],"Compared":[137],"random":[140],"selection":[141],"procedure,":[142],"joint":[144],"application":[145],"novel":[151],"scoring":[152],"scheme":[153],"resulted":[154],"9-fold":[157],"enrichment":[158],"on":[163,202],"first":[165],"rank.":[166],"In":[167],"addition,":[168],"half":[170],"as":[171],"many":[172],"need":[174],"be":[176,193,214],"investigated":[177],"recover":[179],"75%":[180],"our":[186],"dataset.":[187],"Therefore,":[188],"motif-scoring":[190],"should":[192],"helpful":[194],"guide":[196],"experiments":[197],"because":[198],"it":[199],"allows":[200],"focusing":[201],"that":[208],"high":[211],"probability":[212]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
