{"id":"https://openalex.org/W2141726372","doi":"https://doi.org/10.1093/bioinformatics/bts357","title":"Bendix: intuitive helix geometry analysis and abstraction","display_name":"Bendix: intuitive helix geometry analysis and abstraction","publication_year":2012,"publication_date":"2012-06-23","ids":{"openalex":"https://openalex.org/W2141726372","doi":"https://doi.org/10.1093/bioinformatics/bts357","mag":"2141726372","pmid":"https://pubmed.ncbi.nlm.nih.gov/22730430"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts357","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/16/2193/48870029/bioinformatics_28_16_2193.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/28/16/2193/48870029/bioinformatics_28_16_2193.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111406166","display_name":"Anna Caroline E. Dahl","orcid":null},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Anna Caroline E. Dahl","raw_affiliation_strings":["Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082706216","display_name":"Matthieu Chavent","orcid":"https://orcid.org/0000-0003-4524-4773"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthieu Chavent","raw_affiliation_strings":["Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041718990","display_name":"Mark S.P. Sansom","orcid":"https://orcid.org/0000-0001-6360-7959"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark S. P. Sansom","raw_affiliation_strings":["Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5111406166"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6305,"has_fulltext":false,"cited_by_count":140,"citation_normalized_percentile":{"value":0.93890596,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"28","issue":"16","first_page":"2193","last_page":"2194"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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/T10617","display_name":"Cellular transport and secretion","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.6568953990936279},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.6030434370040894},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5684080719947815},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.561090350151062},{"id":"https://openalex.org/keywords/helix","display_name":"Helix (gastropod)","score":0.5539982914924622},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5439382791519165},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5339905619621277},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5233132839202881},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.5096771717071533},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.5019035339355469},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4687766134738922},{"id":"https://openalex.org/keywords/engineering-drawing","display_name":"Engineering drawing","score":0.4413449764251709},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4364604353904724},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4340779781341553},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21392324566841125},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.19487157464027405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14495959877967834},{"id":"https://openalex.org/keywords/geology","display_name":"Geology","score":0.09244021773338318},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07055047154426575}],"concepts":[{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.6568953990936279},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.6030434370040894},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5684080719947815},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.561090350151062},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.5539982914924622},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5439382791519165},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5339905619621277},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5233132839202881},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.5096771717071533},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.5019035339355469},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4687766134738922},{"id":"https://openalex.org/C199639397","wikidata":"https://www.wikidata.org/wiki/Q1788588","display_name":"Engineering drawing","level":1,"score":0.4413449764251709},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4364604353904724},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4340779781341553},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21392324566841125},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.19487157464027405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14495959877967834},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.09244021773338318},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07055047154426575},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D017433","descriptor_name":"Protein Structure, Secondary","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":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/bts357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts357","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/16/2193/48870029/bioinformatics_28_16_2193.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:22730430","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22730430","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:10.1.1.1021.9276","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1021.9276","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/early/2012/06/23/bioinformatics.bts357.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2733961","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3413393","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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:ora.ox.ac.uk:uuid:fa3ac2d4-153b-42be-bc0e-3b6fc5bf91d0","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:fa3ac2d4-153b-42be-bc0e-3b6fc5bf91d0","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symplectic Elements at Oxford","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3413393","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3413393","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts357","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/16/2193/48870029/bioinformatics_28_16_2193.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":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2141726372.pdf","grobid_xml":"https://content.openalex.org/works/W2141726372.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1973111841","https://openalex.org/W1981772705","https://openalex.org/W1998518831","https://openalex.org/W1999467960","https://openalex.org/W2019991560","https://openalex.org/W2029667189","https://openalex.org/W2030947664","https://openalex.org/W2051864856","https://openalex.org/W2083882357","https://openalex.org/W2106207499","https://openalex.org/W2116541825","https://openalex.org/W2121727772","https://openalex.org/W2171268876"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W2045155990","https://openalex.org/W4313163053","https://openalex.org/W3124914020","https://openalex.org/W3045811229","https://openalex.org/W4300973204","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W1483408780","https://openalex.org/W4284884309"],"abstract_inverted_index":{"Bendix":[0,13],"source":[1],"code":[2],"and":[3,23],"documentation,":[4],"including":[5],"installation":[6],"instructions,":[7],"are":[8],"freely":[9],"available":[10],"at":[11],"http://sbcb.bioch.ox.ac.uk/Bendix.":[12],"is":[14,24],"written":[15],"in":[16],"Tcl":[17],"as":[18],"an":[19],"extension":[20],"to":[21],"VMD":[22],"supported":[25],"by":[26],"all":[27],"major":[28],"operating":[29],"systems.":[30]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
