{"id":"https://openalex.org/W2138116388","doi":"https://doi.org/10.1093/bioinformatics/btg006","title":"PDP: protein domain parser","display_name":"PDP: protein domain parser","publication_year":2003,"publication_date":"2003-02-12","ids":{"openalex":"https://openalex.org/W2138116388","doi":"https://doi.org/10.1093/bioinformatics/btg006","mag":"2138116388","pmid":"https://pubmed.ncbi.nlm.nih.gov/12584135"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg006","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/429/718131/btg006.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/19/3/429/718131/btg006.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062487682","display_name":"Nickolai Alexandrov","orcid":"https://orcid.org/0000-0003-3381-0918"},"institutions":[{"id":"https://openalex.org/I1311564700","display_name":"Ceres","ror":"https://ror.org/003sbhj60","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311564700"]},{"id":"https://openalex.org/I200576644","display_name":"HRL Laboratories (United States)","ror":"https://ror.org/05p7te762","country_code":"US","type":"company","lineage":["https://openalex.org/I200576644"]},{"id":"https://openalex.org/I4210120047","display_name":"Ceres Nanosciences","ror":"https://ror.org/02tg35219","country_code":"US","type":"company","lineage":["https://openalex.org/I4210120047"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nickolai Alexandrov","raw_affiliation_strings":["Ceres Inc, 3007 Malibu Canyon Road, Malibu, CA 90265, USA. nicka@ceres-inc.com","Ceres, Inc, 3007 Malibu Canyon Road , Malibu , CA , 90265 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ceres Inc, 3007 Malibu Canyon Road, Malibu, CA 90265, USA. nicka@ceres-inc.com","institution_ids":["https://openalex.org/I1311564700"]},{"raw_affiliation_string":"Ceres, Inc, 3007 Malibu Canyon Road , Malibu , CA , 90265 , USA","institution_ids":["https://openalex.org/I1311564700","https://openalex.org/I200576644","https://openalex.org/I4210120047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077993679","display_name":"Ilya N. Shindyalov","orcid":null},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ilya Shindyalov","raw_affiliation_strings":["SAN DIEGO SUPERCOMPUTER CENTER#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SAN DIEGO SUPERCOMPUTER CENTER#TAB#","institution_ids":["https://openalex.org/I181653535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4928,"has_fulltext":false,"cited_by_count":158,"citation_normalized_percentile":{"value":0.89548256,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"429","last_page":"430"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7732999920845032,"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":0.7732999920845032,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.06729999929666519,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.03610000014305115,"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/computer-science","display_name":"Computer science","score":0.7799776792526245},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.7326618432998657},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7273120880126953},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.6910870671272278},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.606834352016449},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5305346250534058},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.447689026594162},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.36972901225090027},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3245731592178345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11496442556381226},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07021719217300415}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7799776792526245},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.7326618432998657},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7273120880126953},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6910870671272278},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.606834352016449},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5305346250534058},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.447689026594162},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.36972901225090027},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3245731592178345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11496442556381226},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07021719217300415},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"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":"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/btg006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg006","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/429/718131/btg006.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:12584135","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12584135","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/btg006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg006","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/429/718131/btg006.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":[{"id":"https://metadata.un.org/sdg/17","score":0.49000000953674316,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1524556134","https://openalex.org/W1975736414","https://openalex.org/W1998616079","https://openalex.org/W2002195659","https://openalex.org/W2023790301","https://openalex.org/W2045088722","https://openalex.org/W2050152906","https://openalex.org/W2085277871","https://openalex.org/W2108067237","https://openalex.org/W2111374837","https://openalex.org/W2133062651","https://openalex.org/W2141885858","https://openalex.org/W2147805410","https://openalex.org/W2155320925","https://openalex.org/W2166699767"],"related_works":["https://openalex.org/W2169315304","https://openalex.org/W2499073244","https://openalex.org/W2118652015","https://openalex.org/W3197405877","https://openalex.org/W4213112444","https://openalex.org/W1987583739","https://openalex.org/W2029370147","https://openalex.org/W2414304388","https://openalex.org/W2116160060","https://openalex.org/W2405335529"],"abstract_inverted_index":{"UNLABELLED:":[0],"We":[1],"have":[2],"developed":[3],"a":[4,40,51,59],"program":[5,18],"for":[6,61],"automatic":[7,62],"identification":[8],"of":[9,16,33,42,53,77],"domains":[10,71],"in":[11,73],"protein":[12],"three-dimensional":[13],"structures.":[14],"Performance":[15],"the":[17,29],"was":[19],"assessed":[20],"by":[21,26,37,48],"three":[22],"different":[23],"benchmarks:":[24],"(i)":[25],"comparison":[27,38,49],"with":[28,39,50],"expert-curated":[30],"SCOP":[31],"database":[32],"structural":[34],"domains;":[35],"(ii)":[36],"collection":[41],"manual":[43],"domain":[44,63],"assignments;":[45],"and":[46],"(iii)":[47],"set":[52],"55":[54],"proteins,":[55],"frequently":[56],"used":[57],"as":[58],"benchmark":[60],"assignment.":[64],"In":[65],"all":[66],"these":[67],"benchmarks":[68],"PDP":[69],"identified":[70],"correctly":[72],"more":[74],"than":[75],"80%":[76],"proteins.":[78],"AVAILABILITY:":[79],"http://123d.ncifcrf.gov/.":[80]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":9}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
