{"id":"https://openalex.org/W2172175286","doi":"https://doi.org/10.1093/bioinformatics/btm627","title":"Utility library for structural bioinformatics","display_name":"Utility library for structural bioinformatics","publication_year":2008,"publication_date":"2008-01-28","ids":{"openalex":"https://openalex.org/W2172175286","doi":"https://doi.org/10.1093/bioinformatics/btm627","mag":"2172175286","pmid":"https://pubmed.ncbi.nlm.nih.gov/18227118"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm627","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm627","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/584/49045600/bioinformatics_24_4_584.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/24/4/584/49045600/bioinformatics_24_4_584.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013884470","display_name":"Dominik Gront","orcid":"https://orcid.org/0000-0002-2260-2083"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Dominik Gront","raw_affiliation_strings":["University of Warsaw, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"University of Warsaw, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025085688","display_name":"Andrzej Koli\u0144ski","orcid":"https://orcid.org/0000-0002-8830-2315"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Andrzej Kolinski","raw_affiliation_strings":["University of Warsaw, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"University of Warsaw, Faculty of Chemistry, Pasteura 1 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013884470"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.02,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.86595777,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"4","first_page":"584","last_page":"585"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9930999875068665,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9915000200271606,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5716066360473633},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5191206336021423},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4607241451740265},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3250318169593811},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29861122369766235}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5716066360473633},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5191206336021423},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4607241451740265},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3250318169593811},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29861122369766235}],"mesh":[{"descriptor_ui":"D007990","descriptor_name":"Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007990","descriptor_name":"Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007990","descriptor_name":"Libraries","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm627","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm627","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/584/49045600/bioinformatics_24_4_584.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:18227118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18227118","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/btm627","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm627","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/584/49045600/bioinformatics_24_4_584.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2172175286.pdf","grobid_xml":"https://content.openalex.org/works/W2172175286.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1985225270","https://openalex.org/W1992102171","https://openalex.org/W1996423252","https://openalex.org/W2098781592","https://openalex.org/W2130479394","https://openalex.org/W2145904912","https://openalex.org/W2146413057","https://openalex.org/W2150934173","https://openalex.org/W2164671969","https://openalex.org/W2168172687"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"In":[0],"this":[1],"Note":[2],"we":[3],"present":[4],"a":[5,22,85],"new":[6,70],"software":[7,35,90],"library":[8,13],"for":[9,93],"structural":[10,25],"bioinformatics.":[11],"The":[12,34,89],"contains":[14],"programs,":[15],"computing":[16],"sequence-":[17],"and":[18,21,46,110],"profile-based":[19],"alignments":[20],"variety":[23],"of":[24,30,72,96],"calculations":[26],"with":[27],"user-friendly":[28],"handling":[29],"various":[31],"data":[32],"formats.":[33],"organization":[36],"is":[37,91],"very":[38],"flexible.":[39],"Algorithms":[40],"are":[41],"written":[42],"in":[43,65],"Java":[44,51],"language":[45,63],"may":[47],"be":[48,57],"used":[49],"by":[50],"programs.":[52],"Moreover":[53],"the":[54,69],"modules":[55],"can":[56,79],"accessed":[58],"from":[59,84,98],"Jython":[60],"(Python":[61],"scripting":[62],"implemented":[64],"Java)":[66],"scripts.":[67],"Finally,":[68],"version":[71],"BioShell":[73],"delivers":[74],"several":[75],"utility":[76],"programs":[77],"that":[78],"do":[80],"typical":[81],"bioinformatics":[82],"task":[83],"command-line":[86],"level.":[87],"Availability":[88],"available":[92],"download":[94],"free":[95],"charge":[97],"its":[99],"website:":[100],"http://bioshell.chem.uw.edu.pl.":[101],"This":[102],"website":[103],"provides":[104],"also":[105],"numerous":[106],"examples,":[107],"code":[108],"snippets":[109],"API":[111],"documentation.":[112]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":8}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
