{"id":"https://openalex.org/W2071814394","doi":"https://doi.org/10.1093/nar/gkr1150","title":"ccPDB: compilation and creation of data sets from Protein Data Bank","display_name":"ccPDB: compilation and creation of data sets from Protein Data Bank","publication_year":2011,"publication_date":"2011-12-01","ids":{"openalex":"https://openalex.org/W2071814394","doi":"https://doi.org/10.1093/nar/gkr1150","mag":"2071814394","pmid":"https://pubmed.ncbi.nlm.nih.gov/22139939"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr1150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1150","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D486/9479907/gkr1150.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/40/D1/D486/9479907/gkr1150.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022686871","display_name":"Harinder Singh","orcid":"https://orcid.org/0000-0003-4897-9759"},"institutions":[{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I4210147764","display_name":"Institute of Microbial Technology","ror":"https://ror.org/055rjs771","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I4210147764","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"H. Singh","raw_affiliation_strings":["Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India","Council of Scientific and Industrial Research, New Delhi, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India","institution_ids":["https://openalex.org/I4210147764"]},{"raw_affiliation_string":"Council of Scientific and Industrial Research, New Delhi, India","institution_ids":["https://openalex.org/I66760702"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019536569","display_name":"Jagat Chauhan","orcid":"https://orcid.org/0000-0003-4210-6260"},"institutions":[{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I2799982174","display_name":"Open Source Drug Discovery","ror":"https://ror.org/05pvypf90","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I2799351866","https://openalex.org/I2799982174","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"J. S. Chauhan","raw_affiliation_strings":["Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 2Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 and 3The Open Source Drug Discovery (OSDD) Consortium, Council of Scientific and Industrial Research, Anusandhan Bhavan, 2 Rafi Marg, Delhi 110001, India","Council of Scientific and Industrial Research, New Delhi, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 2Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 and 3The Open Source Drug Discovery (OSDD) Consortium, Council of Scientific and Industrial Research, Anusandhan Bhavan, 2 Rafi Marg, Delhi 110001, India","institution_ids":["https://openalex.org/I2799982174"]},{"raw_affiliation_string":"Council of Scientific and Industrial Research, New Delhi, India","institution_ids":["https://openalex.org/I66760702"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046879365","display_name":"M. Michael Gromiha","orcid":"https://orcid.org/0000-0002-1776-4096"},"institutions":[{"id":"https://openalex.org/I2799982174","display_name":"Open Source Drug Discovery","ror":"https://ror.org/05pvypf90","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I2799351866","https://openalex.org/I2799982174","https://openalex.org/I4210134808","https://openalex.org/I66760702"]},{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"M. M. Gromiha","raw_affiliation_strings":["Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 2Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 and 3The Open Source Drug Discovery (OSDD) Consortium, Council of Scientific and Industrial Research, Anusandhan Bhavan, 2 Rafi Marg, Delhi 110001, India","Council of Scientific and Industrial Research, New Delhi, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 2Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 and 3The Open Source Drug Discovery (OSDD) Consortium, Council of Scientific and Industrial Research, Anusandhan Bhavan, 2 Rafi Marg, Delhi 110001, India","institution_ids":["https://openalex.org/I2799982174"]},{"raw_affiliation_string":"Council of Scientific and Industrial Research, New Delhi, India","institution_ids":["https://openalex.org/I66760702"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051938893","display_name":"Gajendra P. S. Raghava","orcid":"https://orcid.org/0000-0002-8902-2876"},"institutions":[{"id":"https://openalex.org/I66760702","display_name":"Council of Scientific and Industrial Research","ror":"https://ror.org/021wm7p51","country_code":"IN","type":"government","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"G. P. S. Raghava","raw_affiliation_strings":["Council of Scientific and Industrial Research, New Delhi, India"],"affiliations":[{"raw_affiliation_string":"Council of Scientific and Industrial Research, New Delhi, India","institution_ids":["https://openalex.org/I66760702"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022686871"],"corresponding_institution_ids":["https://openalex.org/I4210147764","https://openalex.org/I66760702"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.0423,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.754513,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"40","issue":"D1","first_page":"D486","last_page":"D489"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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":0.9980999827384949,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"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":0.920635461807251},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.8379342555999756},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5832993388175964},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5756145715713501},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.552728533744812},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4653404951095581},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45512622594833374},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43335914611816406},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3487060070037842},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.348319947719574},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3379520773887634},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3372321128845215},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32188743352890015},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.21508464217185974},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.20658814907073975},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1518177092075348},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11087745428085327}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.920635461807251},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.8379342555999756},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5832993388175964},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5756145715713501},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.552728533744812},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4653404951095581},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45512622594833374},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43335914611816406},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3487060070037842},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.348319947719574},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3379520773887634},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3372321128845215},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32188743352890015},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.21508464217185974},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.20658814907073975},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1518177092075348},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11087745428085327}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkr1150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1150","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D486/9479907/gkr1150.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:22139939","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22139939","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:open-archive.highwire.org:nar:40/D1/D486","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/D1/D486","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3245168","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3245168","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/gkr1150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1150","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D486/9479907/gkr1150.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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6399999856948853}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2071814394.pdf","grobid_xml":"https://content.openalex.org/works/W2071814394.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1567621547","https://openalex.org/W1967580419","https://openalex.org/W1969412499","https://openalex.org/W2008708467","https://openalex.org/W2009664421","https://openalex.org/W2012072946","https://openalex.org/W2031198583","https://openalex.org/W2051628563","https://openalex.org/W2059215264","https://openalex.org/W2064515831","https://openalex.org/W2097564976","https://openalex.org/W2098770192","https://openalex.org/W2103505761","https://openalex.org/W2116139800","https://openalex.org/W2126103104","https://openalex.org/W2128653811","https://openalex.org/W2140795069","https://openalex.org/W2151550848","https://openalex.org/W2151687360","https://openalex.org/W2152787368","https://openalex.org/W2153153865","https://openalex.org/W2169087593","https://openalex.org/W2170441710"],"related_works":["https://openalex.org/W3126783617","https://openalex.org/W2732388178","https://openalex.org/W3093468851","https://openalex.org/W1897312405","https://openalex.org/W4353055924","https://openalex.org/W2806488847","https://openalex.org/W2121688928","https://openalex.org/W2069319199","https://openalex.org/W2772651271","https://openalex.org/W4388749535"],"abstract_inverted_index":{"ccPDB":[0],"(http://crdd.osdd.net/raghava/ccpdb/)":[1],"is":[2,76],"a":[3,57,62,77,88,95],"database":[4,122],"of":[5,38,49,65,73,97,108,114,119,126],"data":[6,22,41,67,85,127],"sets":[7,23,42,68,86,128],"compiled":[8,21],"from":[9,24,45,69],"the":[10,25,34,46,70],"literature":[11,26],"and":[12,20,36,117,143],"Protein":[13],"Data":[14],"Bank":[15],"(PDB).":[16],"First,":[17],"we":[18,55],"collected":[19],"used":[27],"for":[28,60],"developing":[29],"bioinformatics":[30],"methods":[31],"to":[32,83],"annotate":[33],"structure":[35],"function":[37],"proteins.":[39],"Second,":[40],"were":[43],"derived":[44],"latest":[47],"release":[48,72],"PDB":[50],"using":[51,87],"standard":[52],"protocols.":[53],"Third,":[54],"developed":[56],"powerful":[58],"module":[59,79],"creating":[61],"wide":[63],"range":[64],"customized":[66],"current":[71],"PDB.":[74],"This":[75,121],"flexible":[78],"that":[80],"allows":[81],"users":[82],"create":[84],"simple":[89],"six":[90],"step":[91],"procedure.":[92],"In":[93],"addition,":[94],"number":[96],"web":[98],"services":[99],"have":[100],"been":[101],"integrated":[102],"in":[103],"ccPDB,":[104],"which":[105],"include":[106],"submission":[107],"jobs":[109],"on":[110],"PDB-based":[111],"servers,":[112],"annotation":[113],"protein":[115],"structures":[116],"generation":[118],"patterns.":[120],"maintains":[123],">30":[124],"types":[125],"such":[129],"as":[130],"secondary":[131],"structure,":[132],"tight-turns,":[133],"nucleotide":[134],"interacting":[135,138],"residues,":[136,139],"metals":[137],"DNA/RNA":[140],"binding":[141],"residues":[142],"so":[144],"on.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
