{"id":"https://openalex.org/W2874062053","doi":"https://doi.org/10.1093/bioinformatics/bty579","title":"PepBDB: a comprehensive structural database of biological peptide\u2013protein interactions","display_name":"PepBDB: a comprehensive structural database of biological peptide\u2013protein interactions","publication_year":2018,"publication_date":"2018-07-04","ids":{"openalex":"https://openalex.org/W2874062053","doi":"https://doi.org/10.1093/bioinformatics/bty579","mag":"2874062053","pmid":"https://pubmed.ncbi.nlm.nih.gov/29982280"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty579","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty579","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/175/48962736/bioinformatics_35_1_175.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/35/1/175/48962736/bioinformatics_35_1_175.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012876890","display_name":"Zeyu Wen","orcid":"https://orcid.org/0000-0003-2221-8628"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zeyu Wen","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059824731","display_name":"Jiahua He","orcid":"https://orcid.org/0000-0002-9075-4978"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahua He","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051853189","display_name":"Huanyu Tao","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huanyu Tao","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053305024","display_name":"Sheng\u2010You Huang","orcid":"https://orcid.org/0000-0002-4209-4565"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sheng-You Huang","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053305024"],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1505,"has_fulltext":true,"cited_by_count":97,"citation_normalized_percentile":{"value":0.7764132,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"35","issue":"1","first_page":"175","last_page":"177"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.41940000653266907,"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":0.41940000653266907,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.09239999949932098,"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":0.09009999781847,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7770929336547852},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.7047926783561707},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.7035122513771057},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6280191540718079},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.5394962430000305},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5343360900878906},{"id":"https://openalex.org/keywords/database-search-engine","display_name":"Database search engine","score":0.4826853275299072},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.46484678983688354},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43391963839530945},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3984786868095398},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2845596969127655},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25437766313552856},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24392852187156677},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.19153553247451782},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14065590500831604},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.09196093678474426},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.0714581310749054}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7770929336547852},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.7047926783561707},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.7035122513771057},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6280191540718079},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.5394962430000305},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5343360900878906},{"id":"https://openalex.org/C48000682","wikidata":"https://www.wikidata.org/wiki/Q5227411","display_name":"Database search engine","level":3,"score":0.4826853275299072},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.46484678983688354},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43391963839530945},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3984786868095398},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2845596969127655},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25437766313552856},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24392852187156677},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.19153553247451782},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14065590500831604},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.09196093678474426},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0714581310749054},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty579","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty579","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/175/48962736/bioinformatics_35_1_175.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:29982280","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29982280","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/bty579","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty579","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/175/48962736/bioinformatics_35_1_175.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":[{"id":"https://openalex.org/G7476102074","display_name":null,"funder_award_id":"2016YFC1305805","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7582944686","display_name":null,"funder_award_id":"2016YFC1305800","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7618829171","display_name":"\u86cb\u767d\u8d28\u76f8\u4e92\u4f5c\u7528\u7684\u591a\u4f53\u5173\u8054\u6548\u5e94\u548c\u5206\u5b50\u67d4\u6027\u7814\u7a76","funder_award_id":"31670724","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321883","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2874062053.pdf","grobid_xml":"https://content.openalex.org/works/W2874062053.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1768303176","https://openalex.org/W2011703027","https://openalex.org/W2015292449","https://openalex.org/W2017793317","https://openalex.org/W2023272942","https://openalex.org/W2041449172","https://openalex.org/W2049091299","https://openalex.org/W2050749891","https://openalex.org/W2054394841","https://openalex.org/W2074473216","https://openalex.org/W2081992461","https://openalex.org/W2083747978","https://openalex.org/W2113617961","https://openalex.org/W2114512254","https://openalex.org/W2130479394","https://openalex.org/W2156876686","https://openalex.org/W2520917239","https://openalex.org/W2562674913","https://openalex.org/W2609643846","https://openalex.org/W2615136515","https://openalex.org/W2799876761","https://openalex.org/W6654087933"],"related_works":["https://openalex.org/W3126783617","https://openalex.org/W2732388178","https://openalex.org/W3093468851","https://openalex.org/W4353055924","https://openalex.org/W2806488847","https://openalex.org/W2121688928","https://openalex.org/W2772651271","https://openalex.org/W4388749535","https://openalex.org/W2793317762","https://openalex.org/W4361279638"],"abstract_inverted_index":{"Summary:":[0],"A":[1],"structural":[2],"database":[3,30,93],"of":[4,23,31,63,97],"peptide-protein":[5,33,85],"interactions":[6],"is":[7,36,109],"important":[8],"for":[9,20,45],"drug":[10,52],"discovery":[11],"targeting":[12],"peptide-mediated":[13],"interactions.":[14],"Although":[15],"some":[16],"peptide":[17],"databases,":[18],"especially":[19],"special":[21],"types":[22],"peptides,":[24],"have":[25,56],"been":[26],"developed,":[27],"a":[28,95],"comprehensive":[29],"cleaned":[32,41,77],"complex":[34,65],"structures":[35,42,66,78],"still":[37],"not":[38,75],"available.":[39],"Such":[40],"are":[43],"valuable":[44],"docking":[46],"and":[47,87,99,106],"scoring":[48],"studies":[49],"in":[50],"structure-based":[51],"design.":[53],"Here,":[54],"we":[55],"developed":[57],"PepBDB-a":[58],"curated":[59],"Peptide":[60],"Binding":[61],"DataBase":[62],"biological":[64,84],"from":[67],"the":[68,92,102],"Protein":[69],"Data":[70],"Bank":[71],"(PDB).":[72],"PepBDB":[73,108],"presents":[74],"only":[76],"but":[79],"also":[80],"extensive":[81],"information":[82],"about":[83],"interactions,":[86],"allows":[88],"users":[89],"to":[90],"search":[91,103],"with":[94],"variety":[96],"options":[98],"interactively":[100],"visualize":[101],"results.":[104],"Availability":[105],"implementation:":[107],"available":[110],"at":[111],"http://huanglab.phys.hust.edu.cn/pepbdb/.":[112]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":26},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
