{"id":"https://openalex.org/W1977266578","doi":"https://doi.org/10.1093/nar/gkn270","title":"soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts","display_name":"soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts","publication_year":2008,"publication_date":"2008-05-16","ids":{"openalex":"https://openalex.org/W1977266578","doi":"https://doi.org/10.1093/nar/gkn270","mag":"1977266578","pmid":"https://pubmed.ncbi.nlm.nih.gov/18487276"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn270","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn270","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W252/7626905/gkn270.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W252/7626905/gkn270.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007820143","display_name":"Charles A. Lesburg","orcid":"https://orcid.org/0000-0001-7245-7331"},"institutions":[{"id":"https://openalex.org/I2801558778","display_name":"LabCorp (United States)","ror":"https://ror.org/03zsdhz84","country_code":"US","type":"company","lineage":["https://openalex.org/I2801558778"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"C. A. Lesburg","raw_affiliation_strings":["Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. charles.lesburg@spcorp.com","Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA"],"affiliations":[{"raw_affiliation_string":"Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. charles.lesburg@spcorp.com","institution_ids":["https://openalex.org/I2801558778"]},{"raw_affiliation_string":"Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001778051","display_name":"Jos\u00e9 S. Duca","orcid":"https://orcid.org/0000-0002-0880-5618"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. S. Duca","raw_affiliation_strings":["Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA"],"affiliations":[{"raw_affiliation_string":"Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5007820143"],"corresponding_institution_ids":["https://openalex.org/I2801558778"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.2752,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5866866,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"36","issue":"Web Server","first_page":"W252","last_page":"W254"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9922999739646912,"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":0.9918000102043152,"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/biology","display_name":"Biology","score":0.8859042525291443},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4944617748260498},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3750680685043335},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3554953932762146},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.17922663688659668}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8859042525291443},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4944617748260498},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3750680685043335},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3554953932762146},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.17922663688659668}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":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":"D034742","descriptor_name":"Electronic Mail","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034742","descriptor_name":"Electronic Mail","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034742","descriptor_name":"Electronic Mail","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkn270","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn270","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W252/7626905/gkn270.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18487276","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18487276","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2447792","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447792","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn270","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn270","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W252/7626905/gkn270.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311175","display_name":"Steadman Philippon Research Institute","ror":"https://ror.org/03msykc12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1977266578.pdf","grobid_xml":"https://content.openalex.org/works/W1977266578.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1571376639","https://openalex.org/W1995808589","https://openalex.org/W2055043387","https://openalex.org/W2130479394","https://openalex.org/W2166458835","https://openalex.org/W2993222596","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191"],"abstract_inverted_index":{"soaPDB":[0,47,55],"is":[1,21,48,56,65],"a":[2,24,34],"web":[3,25,45],"application":[4],"that":[5],"allows":[6],"generation":[7],"and":[8,14,31,53,64],"organization":[9],"of":[10],"saved":[11],"PDB":[12,29],"searches,":[13],"offers":[15],"automatic":[16],"email":[17],"alerts.":[18],"This":[19],"tool":[20],"used":[22],"from":[23],"interface":[26],"to":[27,50],"store":[28],"searches":[30],"results":[32],"in":[33],"backend":[35],"relational":[36],"database.":[37],"Written":[38],"using":[39],"the":[40],"Ruby":[41],"on":[42],"Rails":[43],"open-source":[44],"framework,":[46],"easy":[49],"deploy,":[51],"maintain":[52],"customize.":[54],"freely":[57],"available":[58,67],"upon":[59],"request":[60],"for":[61],"local":[62],"installation":[63],"also":[66],"at":[68],"http://soapdb.dyndns.org:3000.":[69]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
