{"id":"https://openalex.org/W2170455609","doi":"https://doi.org/10.1093/bioinformatics/btu838","title":"Knowledge-based modeling of peptides at protein interfaces: PiPreD","display_name":"Knowledge-based modeling of peptides at protein interfaces: PiPreD","publication_year":2014,"publication_date":"2014-12-23","ids":{"openalex":"https://openalex.org/W2170455609","doi":"https://doi.org/10.1093/bioinformatics/btu838","mag":"2170455609","pmid":"https://pubmed.ncbi.nlm.nih.gov/25540186"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu838","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu838","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1405/49013753/bioinformatics_31_9_1405.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/31/9/1405/49013753/bioinformatics_31_9_1405.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111840557","display_name":"Baldo Oliva","orcid":null},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Baldo Oliva","raw_affiliation_strings":["Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090989775","display_name":"Narc\u00eds Fern\u00e1ndez\u2010Fuentes","orcid":"https://orcid.org/0000-0002-6421-1080"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Narcis Fernandez-Fuentes","raw_affiliation_strings":["Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090989775"],"corresponding_institution_ids":["https://openalex.org/I170486558"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.52,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.65324708,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"9","first_page":"1405","last_page":"1410"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3824999928474426,"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":0.3824999928474426,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.0982000008225441,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0697999969124794,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.7426536083221436},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.732173502445221},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.633879542350769},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6168702244758606},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5468066930770874},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5121438503265381},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.44136473536491394},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.32500001788139343},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25920015573501587},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16433945298194885},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1461591124534607},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.129143625497818}],"concepts":[{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.7426536083221436},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.732173502445221},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.633879542350769},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6168702244758606},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5468066930770874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5121438503265381},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.44136473536491394},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.32500001788139343},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25920015573501587},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16433945298194885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1461591124534607},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.129143625497818},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"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":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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},{"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":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu838","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu838","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1405/49013753/bioinformatics_31_9_1405.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:25540186","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25540186","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/btu838","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu838","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1405/49013753/bioinformatics_31_9_1405.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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170455609.pdf","grobid_xml":"https://content.openalex.org/works/W2170455609.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1495033819","https://openalex.org/W1824220821","https://openalex.org/W1909149576","https://openalex.org/W1967224365","https://openalex.org/W1974746017","https://openalex.org/W1992864103","https://openalex.org/W1994859764","https://openalex.org/W1995808589","https://openalex.org/W2008845432","https://openalex.org/W2012575827","https://openalex.org/W2012987401","https://openalex.org/W2017086893","https://openalex.org/W2023272942","https://openalex.org/W2023391220","https://openalex.org/W2024947155","https://openalex.org/W2026711123","https://openalex.org/W2041449172","https://openalex.org/W2054711926","https://openalex.org/W2056169996","https://openalex.org/W2059942519","https://openalex.org/W2065617298","https://openalex.org/W2066714607","https://openalex.org/W2074105113","https://openalex.org/W2075770210","https://openalex.org/W2080022084","https://openalex.org/W2081320767","https://openalex.org/W2083695927","https://openalex.org/W2088877201","https://openalex.org/W2097933346","https://openalex.org/W2102709986","https://openalex.org/W2104538433","https://openalex.org/W2109604654","https://openalex.org/W2110803021","https://openalex.org/W2116890528","https://openalex.org/W2127248667","https://openalex.org/W2132439221","https://openalex.org/W2135579845","https://openalex.org/W2142454421","https://openalex.org/W2144265524","https://openalex.org/W2151550848","https://openalex.org/W2156379460","https://openalex.org/W2159826634","https://openalex.org/W2201713963","https://openalex.org/W2265106521"],"related_works":["https://openalex.org/W2046765700","https://openalex.org/W4384345686","https://openalex.org/W262455470","https://openalex.org/W4242899858","https://openalex.org/W2145834781","https://openalex.org/W2914490533","https://openalex.org/W2021213676","https://openalex.org/W1970785155","https://openalex.org/W1832993298","https://openalex.org/W4388831384"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein-protein":[1],"interactions":[2],"(PPIs)":[3],"underpin":[4],"virtually":[5],"all":[6],"cellular":[7],"processes":[8],"both":[9],"in":[10],"health":[11],"and":[12,57,73,84,110,134,148,151],"disease.":[13],"Modulating":[14],"the":[15,46,92,99,102,113,122,126,131,139,158],"interaction":[16],"between":[17],"proteins":[18],"by":[19,91],"means":[20],"of":[21,48,76,94,101,141],"small":[22],"(chemical)":[23],"agents":[24,44],"is":[25],"therefore":[26],"a":[27,53,71,85],"promising":[28],"route":[29],"for":[30,45,121,138],"future":[31],"novel":[32,54],"therapeutic":[33],"interventions.":[34],"In":[35],"this":[36],"context,":[37],"peptides":[38,63],"are":[39,153],"gaining":[40],"momentum":[41],"as":[42],"emerging":[43],"modulation":[47],"PPIs.":[49],"RESULTS:":[50],"We":[51],"reported":[52],"computational,":[55],"structure":[56],"knowledge-based":[58],"approach":[59],"to":[60,64,157],"model":[61],"orthosteric":[62],"target":[65,104],"PPIs:":[66],"PiPreD.":[67],"PiPreD":[68,108,129],"relies":[69],"on":[70,98,125],"precompiled":[72],"bespoken":[74],"library":[75],"structural":[77,87],"motifs,":[78],"iMotifs,":[79],"extracted":[80],"from":[81],"protein":[82,103,127],"complexes":[83],"fast":[86],"modeling":[88],"algorithm":[89],"driven":[90],"location":[93],"native":[95],"chemical":[96],"groups":[97],"interface":[100,115],"named":[105],"anchor":[106],"residues.":[107],"comprehensive":[109],"systematically":[111],"samples":[112],"entire":[114],"deriving":[116],"peptide":[117],"conformations":[118],"best":[119],"suited":[120],"given":[123],"region":[124],"interface.":[128],"complements":[130],"existing":[132],"technologies":[133],"provides":[135],"new":[136],"solutions":[137],"disruption":[140],"selected":[142],"interactions.":[143],"AVAILABILITY":[144],"AND":[145],"IMPLEMENTATION:":[146],"Database":[147],"accessory":[149],"scripts":[150],"programs":[152],"available":[154],"upon":[155],"request":[156],"authors":[159],"or":[160],"at":[161],"http://www.bioinsilico.org/PIPRED.":[162],"CONTACT:":[163],"narcis.fernandez@gmail.com.":[164]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":4}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
