{"id":"https://openalex.org/W2100641899","doi":"https://doi.org/10.1093/bioinformatics/18.1.209","title":"PCSB\u2014a program collection for structural biology and biophysical chemistry","display_name":"PCSB\u2014a program collection for structural biology and biophysical chemistry","publication_year":2002,"publication_date":"2002-01-01","ids":{"openalex":"https://openalex.org/W2100641899","doi":"https://doi.org/10.1093/bioinformatics/18.1.209","mag":"2100641899","pmid":"https://pubmed.ncbi.nlm.nih.gov/11836236"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/18.1.209","doi":"https://doi.org/10.1093/bioinformatics/18.1.209","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/18.1.209","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/18/1/209/48850395/bioinformatics_18_1_209.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,"listed_in":["abdc-a","cwts-core","doaj","doyens","jufo-3","ki-jl-2","medline","norway-2"],"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"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/18/1/209/48850395/bioinformatics_18_1_209.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025007734","display_name":"Andreas Hofmann","orcid":"https://orcid.org/0000-0003-4408-5467","observed_orcids":["https://orcid.org/0000-0003-4408-5467"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Hofmann","raw_affiliation_strings":["Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA","Macromolecular Crystallography Laboratory, NCI at Frederick,#N# Frederick, MD 21702, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Macromolecular Crystallography Laboratory, NCI at Frederick,#N# Frederick, MD 21702, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027980832","display_name":"Alexander Wlodawer","orcid":"https://orcid.org/0000-0002-5510-9703","observed_orcids":["https://orcid.org/0000-0002-5510-9703"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Wlodawer","raw_affiliation_strings":["Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA","Macromolecular Crystallography Laboratory, NCI at Frederick,#N# Frederick, MD 21702, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Macromolecular Crystallography Laboratory, NCI at Frederick,#N# Frederick, MD 21702, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.71,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.70888591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"18","issue":"1","first_page":"209","last_page":"210"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.7860999703407288,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.7860999703407288,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.20720000565052032,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/java-classes","display_name":"Java classes","score":0.7739999890327454},{"id":"https://openalex.org/keywords/biophysical-chemistry","display_name":"biophysical chemistry","score":0.9150000214576721},{"id":"https://openalex.org/keywords/matrix-vector-operations","display_name":"matrix-vector operations","score":0.9330000281333923},{"id":"https://openalex.org/keywords/crystal-symmetry","display_name":"crystal symmetry","score":0.9559999704360962},{"id":"https://openalex.org/keywords/pdb-file-parsing","display_name":"PDB file parsing","score":0.9340000152587891},{"id":"https://openalex.org/keywords/object-oriented-programming","display_name":"object-oriented programming","score":0.9110000133514404}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.8148431777954102},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8086338043212891},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6819530725479126},{"id":"https://openalex.org/C73752529","wikidata":"https://www.wikidata.org/wiki/Q79872","display_name":"Object-oriented programming","level":2,"score":0.5181975960731506},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.36378371715545654},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3451443016529083}],"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":"D002627","descriptor_name":"Chemistry, Physical","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D002627","descriptor_name":"Chemistry, Physical","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D002627","descriptor_name":"Chemistry, Physical","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/18.1.209","doi":"https://doi.org/10.1093/bioinformatics/18.1.209","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/18.1.209","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/18/1/209/48850395/bioinformatics_18_1_209.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,"listed_in":["abdc-a","cwts-core","doaj","doyens","jufo-3","ki-jl-2","medline","norway-2"],"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:11836236","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11836236","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,"listed_in":[],"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":"Journal Article"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/22213","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10072/22213","pdf_url":null,"source":{"id":"https://openalex.org/S7407064376","display_name":"Griffith Research Online","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/18.1.209","doi":"https://doi.org/10.1093/bioinformatics/18.1.209","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/18.1.209","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/18/1/209/48850395/bioinformatics_18_1_209.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,"listed_in":["abdc-a","cwts-core","doaj","doyens","jufo-3","ki-jl-2","medline","norway-2"],"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":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100641899.pdf","grobid_xml":"https://content.openalex.org/works/W2100641899.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2005986251","https://openalex.org/W2014694459","https://openalex.org/W2132905138","https://openalex.org/W2136567909","https://openalex.org/W2323174283"],"related_works":["https://openalex.org/W2749690376","https://openalex.org/W4281673905","https://openalex.org/W2788563018","https://openalex.org/W2786317006","https://openalex.org/W2997587123","https://openalex.org/W1578809901","https://openalex.org/W2611825707","https://openalex.org/W1547394117","https://openalex.org/W1580516753","https://openalex.org/W2552002334"],"abstract_inverted_index":{"Abstract":[0],"We":[1],"present":[2,84],"the":[3,12,65,85,101,109,122,128],"first":[4,86],"package":[5],"of":[6,14,25,36,89],"Java":[7,27,102,123],"classes":[8,28,124],"specifically":[9],"aimed":[10],"at":[11],"handling":[13,77],"structural":[15,81],"and":[16,44,57,73,98],"biophysical":[17],"problems.":[18],"To":[19,136],"enable":[20],"object-oriented":[21],"programming":[22],"a":[23],"basis":[24],"fundamental":[26],"is":[29,130],"required":[30],"which":[31,49],"deals":[32],"with":[33,60],"basic":[34,53],"operations":[35],"vectors,":[37],"matrices,":[38],"amino":[39],"acid":[40],"sequences,":[41],"crystal":[42],"symmetries":[43],"PDB":[45],"files.":[46],"Five":[47],"classes,":[48],"carry":[50],"out":[51],"these":[52],"operations,":[54],"were":[55],"constructed":[56],"bundled":[58],"together":[59],"several":[61],"utility":[62],"functions":[63],"in":[64,80],"PCSB":[66,120],"package.":[67],"Furthermore,":[68],"to":[69,74,95,105],"demonstrate":[70],"their":[71],"applicability":[72],"obtain":[75],"programs":[76],"common":[78],"tasks":[79],"laboratories,":[82],"we":[83],"six":[87],"applications":[88,92,129],"PCSB.":[90],"All":[91],"are":[93],"portable":[94],"different":[96],"platforms":[97],"require":[99],"only":[100],"Runtime":[103],"Environment":[104],"be":[106,140],"installed":[107],"on":[108],"system.":[110],"Availability:":[111],"http://www24.brinkster.com/hofmanna/pcsb/":[112],"Contact:":[113],"hofmanna@ncifcrf.gov":[114],"Supplementary":[115],"information:":[116],"A":[117],"manual":[118],"for":[119],"describing":[121],"as":[125,127,132],"well":[126],"available":[131],"PDF":[133],"file.":[134],"*":[135],"whom":[137],"correspondence":[138],"should":[139],"addressed.":[141]},"counts_by_year":[{"year":2019,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-09-06T09:10:53.072986","created_date":"2025-10-10T00:00:00"}