{"id":"https://openalex.org/W2100017567","doi":"https://doi.org/10.1093/bioinformatics/btt032","title":"BION web server: predicting non-specifically bound surface ions","display_name":"BION web server: predicting non-specifically bound surface ions","publication_year":2013,"publication_date":"2013-02-03","ids":{"openalex":"https://openalex.org/W2100017567","doi":"https://doi.org/10.1093/bioinformatics/btt032","mag":"2100017567","pmid":"https://pubmed.ncbi.nlm.nih.gov/23380591"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt032","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/805/48901654/bioinformatics_29_6_805.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/29/6/805/48901654/bioinformatics_29_6_805.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066047116","display_name":"Marharyta Petukh","orcid":"https://orcid.org/0000-0001-8473-5677"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marharyta Petukh","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012257092","display_name":"Taylor Kimmet","orcid":null},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taylor Kimmet","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075727451","display_name":"Emil Alexov","orcid":"https://orcid.org/0000-0001-5346-0156"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emil Alexov","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5075727451"],"corresponding_institution_ids":["https://openalex.org/I8078737"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.2516,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.78490864,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"29","issue":"6","first_page":"805","last_page":"806"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9994999766349792,"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":0.9994999766349792,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9994000196456909,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9972000122070312,"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/computer-science","display_name":"Computer science","score":0.6844654679298401},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.6760629415512085},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6504650712013245},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.6050230860710144},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.6049918532371521},{"id":"https://openalex.org/keywords/upper-and-lower-bounds","display_name":"Upper and lower bounds","score":0.5750061869621277},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.5317517518997192},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.44776543974876404},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.28960904479026794},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2714509963989258},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2611665725708008},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1633334457874298},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.08319729566574097}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6844654679298401},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.6760629415512085},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6504650712013245},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.6050230860710144},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.6049918532371521},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.5750061869621277},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.5317517518997192},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.44776543974876404},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.28960904479026794},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2714509963989258},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2611665725708008},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1633334457874298},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.08319729566574097},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"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":"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":"D007477","descriptor_name":"Ions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","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":"D011506","descriptor_name":"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":"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":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt032","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/805/48901654/bioinformatics_29_6_805.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:23380591","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23380591","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2934687","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3597141","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:pubmedcentral.nih.gov:3597141","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3597141","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/btt032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt032","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/805/48901654/bioinformatics_29_6_805.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":[{"id":"https://openalex.org/G3233386537","display_name":null,"funder_award_id":"R01GM093937","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100017567.pdf","grobid_xml":"https://content.openalex.org/works/W2100017567.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1976190421","https://openalex.org/W1983259744","https://openalex.org/W2004145462","https://openalex.org/W2007258535","https://openalex.org/W2029263948","https://openalex.org/W2035583659","https://openalex.org/W2043917273","https://openalex.org/W2062335580","https://openalex.org/W2079666836","https://openalex.org/W2081399318","https://openalex.org/W2147993766","https://openalex.org/W3107088716"],"related_works":["https://openalex.org/W3013085049","https://openalex.org/W1560496689","https://openalex.org/W4386900933","https://openalex.org/W4385301946","https://openalex.org/W4297797135","https://openalex.org/W3125672081","https://openalex.org/W1673581201","https://openalex.org/W2991991550","https://openalex.org/W64182352","https://openalex.org/W4289799755"],"abstract_inverted_index":{"MOTIVATION:":[0],"Ions":[1],"are":[2,10,56,88,93],"essential":[3],"component":[4],"of":[5,22,79],"the":[6,69,75,114,135],"cell":[7],"and":[8,33,113,137],"frequently":[9],"found":[11],"bound":[12,58,82,130],"to":[13,18,25,35,59,95,101,110,122],"various":[14],"macromolecules,":[15],"in":[16,40],"particular":[17],"proteins.":[19],"A":[20],"binding":[21],"an":[23],"ion":[24],"a":[26,66],"protein":[27],"greatly":[28],"affects":[29],"protein's":[30],"biophysical":[31],"characteristics":[32],"needs":[34],"be":[36,49,111],"taken":[37],"into":[38],"account":[39],"any":[41],"modeling":[42],"approach.":[43],"However,":[44],"ion's":[45],"bounded":[46],"positions":[47],"cannot":[48],"easily":[50],"revealed":[51],"experimentally,":[52],"especially":[53],"if":[54],"they":[55,92],"loosely":[57],"macromolecular":[60],"surface.":[61],"RESULTS:":[62],"Here,":[63],"we":[64],"report":[65],"web":[67,71,103],"server,":[68,72],"BION":[70,98],"which":[73,85],"addresses":[74],"demand":[76],"for":[77,84,140],"tools":[78],"predicting":[80],"surface":[81],"ions,":[83],"specific":[86],"interactions":[87],"not":[89],"crucial;":[90],"thus,":[91],"difficult":[94],"predict.":[96],"The":[97,125],"is":[99,116,132,138],"easy":[100,121],"use":[102],"server":[104],"that":[105],"requires":[106],"only":[107],"coordinate":[108,126],"file":[109,127],"inputted,":[112],"user":[115],"provided":[117],"with":[118,128],"various,":[119],"but":[120],"navigate,":[123],"options.":[124],"predicted":[129],"ions":[131],"displayed":[133],"on":[134],"output":[136],"available":[139],"download.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}