{"id":"https://openalex.org/W2121054327","doi":"https://doi.org/10.1093/bioinformatics/btg292","title":"Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins","display_name":"Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins","publication_year":2003,"publication_date":"2003-11-01","ids":{"openalex":"https://openalex.org/W2121054327","doi":"https://doi.org/10.1093/bioinformatics/btg292","mag":"2121054327","pmid":"https://pubmed.ncbi.nlm.nih.gov/14594717"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg292","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg292","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/16/2112/48904640/bioinformatics_19_16_2112.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/19/16/2112/48904640/bioinformatics_19_16_2112.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058131399","display_name":"Kristian Rother","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kristian Rother","raw_affiliation_strings":["Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University, Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University, Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043414157","display_name":"Robert Prei\u00dfner","orcid":"https://orcid.org/0000-0002-2407-1087"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Robert Preissner","raw_affiliation_strings":["Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany","Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University,"],"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062823306","display_name":"Andrean Goede","orcid":"https://orcid.org/0000-0002-9044-9869"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andrean Goede","raw_affiliation_strings":["Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany","Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University,"],"affiliations":[{"raw_affiliation_string":"Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112588600","display_name":"Cornelius Fr\u00f6mmel","orcid":null},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Cornelius Fr\u00f6mmel","raw_affiliation_strings":["Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University,","Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University,","institution_ids":[]},{"raw_affiliation_string":"Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5112588600"],"corresponding_institution_ids":["https://openalex.org/I7877124"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8007,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.70424305,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":"16","first_page":"2112","last_page":"2121"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9976000189781189,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"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/distribution","display_name":"Distribution (mathematics)","score":0.5451802611351013},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.5023353099822998},{"id":"https://openalex.org/keywords/sphere-packing","display_name":"Sphere packing","score":0.4637029767036438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41902586817741394},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3471868634223938},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.338762104511261},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2822147309780121},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.27416229248046875},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24465706944465637},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.2227376401424408},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.12505993247032166}],"concepts":[{"id":"https://openalex.org/C110121322","wikidata":"https://www.wikidata.org/wiki/Q865811","display_name":"Distribution (mathematics)","level":2,"score":0.5451802611351013},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5023353099822998},{"id":"https://openalex.org/C183893376","wikidata":"https://www.wikidata.org/wiki/Q900117","display_name":"Sphere packing","level":2,"score":0.4637029767036438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41902586817741394},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3471868634223938},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.338762104511261},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2822147309780121},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.27416229248046875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24465706944465637},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.2227376401424408},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.12505993247032166}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D016880","descriptor_name":"Anisotropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016880","descriptor_name":"Anisotropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016880","descriptor_name":"Anisotropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022081","descriptor_name":"Cell Surface Extensions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022081","descriptor_name":"Cell Surface Extensions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022081","descriptor_name":"Cell Surface Extensions","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btg292","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg292","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/16/2112/48904640/bioinformatics_19_16_2112.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:14594717","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14594717","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},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.619.393","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.619.393","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/19/16/2112.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.646.9990","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.646.9990","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/goede2.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg292","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg292","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/16/2112/48904640/bioinformatics_19_16_2112.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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2121054327.pdf","grobid_xml":"https://content.openalex.org/works/W2121054327.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W59526888","https://openalex.org/W255996521","https://openalex.org/W1520127302","https://openalex.org/W1964052558","https://openalex.org/W1966401562","https://openalex.org/W1967747296","https://openalex.org/W1980705387","https://openalex.org/W2000224444","https://openalex.org/W2004286074","https://openalex.org/W2024243556","https://openalex.org/W2029820720","https://openalex.org/W2034746027","https://openalex.org/W2036323298","https://openalex.org/W2048053380","https://openalex.org/W2050587751","https://openalex.org/W2062351773","https://openalex.org/W2063831812","https://openalex.org/W2069297570","https://openalex.org/W2076394025","https://openalex.org/W2081670113","https://openalex.org/W2083654158","https://openalex.org/W2098644398","https://openalex.org/W2103594991","https://openalex.org/W2105902442","https://openalex.org/W2106337622","https://openalex.org/W2107694043","https://openalex.org/W2113623846","https://openalex.org/W2114370367","https://openalex.org/W2117077088","https://openalex.org/W2119236577","https://openalex.org/W2120372728","https://openalex.org/W2154031461","https://openalex.org/W2155373599","https://openalex.org/W2159294509","https://openalex.org/W2162166182","https://openalex.org/W3148526999","https://openalex.org/W4235848672"],"related_works":["https://openalex.org/W1993644547","https://openalex.org/W2008929884","https://openalex.org/W2015783910","https://openalex.org/W1969605115","https://openalex.org/W2077730636","https://openalex.org/W195484974","https://openalex.org/W2358963587","https://openalex.org/W2299153117","https://openalex.org/W2983322931","https://openalex.org/W2804416670"],"abstract_inverted_index":{"Calculation":[0],"software":[1],"and":[2],"detailed":[3],"packing":[4],"data":[5],"are":[6],"available":[7],"on":[8],"request.":[9]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
