{"id":"https://openalex.org/W2106956326","doi":"https://doi.org/10.1093/bioinformatics/bts200","title":"DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol","display_name":"DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol","publication_year":2012,"publication_date":"2012-04-23","ids":{"openalex":"https://openalex.org/W2106956326","doi":"https://doi.org/10.1093/bioinformatics/bts200","mag":"2106956326","pmid":"https://pubmed.ncbi.nlm.nih.gov/22531215"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts200","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts200","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1655/48876448/bioinformatics_28_12_1655.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/28/12/1655/48876448/bioinformatics_28_12_1655.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065725786","display_name":"Nicholas Smith","orcid":"https://orcid.org/0009-0000-7595-5635"},"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":"Nicholas Smith","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078780135","display_name":"Shawn Witham","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":"Shawn Witham","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110276518","display_name":"Subhra Sarkar","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":"Subhra Sarkar","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100436697","display_name":"Jie Zhang","orcid":"https://orcid.org/0000-0002-1028-6765"},"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":"Jie Zhang","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100459657","display_name":"Lin Li","orcid":"https://orcid.org/0000-0001-8645-0392"},"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":"Lin Li","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100404407","display_name":"Chuan Li","orcid":"https://orcid.org/0000-0001-7587-1343"},"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":"Chuan Li","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, 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":false,"raw_author_name":"Emil Alexov","raw_affiliation_strings":["1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biophysics and Bioinformatics, Department of Physics and 2Department of Computer Science, Clemson University, Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5065725786"],"corresponding_institution_ids":["https://openalex.org/I8078737"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.2946,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.9327307,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"12","first_page":"1655","last_page":"1657"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.9692000150680542,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.9692000150680542,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9567000269889832,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9240999817848206,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.6902310848236084},{"id":"https://openalex.org/keywords/delphi","display_name":"Delphi","score":0.6895232796669006},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6874939203262329},{"id":"https://openalex.org/keywords/style","display_name":"Style (visual arts)","score":0.5232842564582825},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.45682623982429504},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3769422173500061},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33282777667045593},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07752707600593567},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.07314038276672363},{"id":"https://openalex.org/keywords/archaeology","display_name":"Archaeology","score":0.06674733757972717}],"concepts":[{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.6902310848236084},{"id":"https://openalex.org/C2779495148","wikidata":"https://www.wikidata.org/wiki/Q487378","display_name":"Delphi","level":2,"score":0.6895232796669006},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6874939203262329},{"id":"https://openalex.org/C2776445246","wikidata":"https://www.wikidata.org/wiki/Q1792644","display_name":"Style (visual arts)","level":2,"score":0.5232842564582825},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.45682623982429504},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3769422173500061},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33282777667045593},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07752707600593567},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.07314038276672363},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.06674733757972717},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","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":"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":"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":"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":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049329","descriptor_name":"Nanostructures","qualifier_ui":"Q000032","qualifier_name":"analysis","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/bts200","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts200","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1655/48876448/bioinformatics_28_12_1655.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:22531215","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22531215","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:europepmc.org:2678123","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3371833","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:3371833","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3371833","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/bts200","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts200","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1655/48876448/bioinformatics_28_12_1655.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/W2106956326.pdf","grobid_xml":"https://content.openalex.org/works/W2106956326.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2040474140","https://openalex.org/W2083364776","https://openalex.org/W2103449051","https://openalex.org/W2110562802","https://openalex.org/W2120715487","https://openalex.org/W2129125660","https://openalex.org/W2152486318","https://openalex.org/W2165759309","https://openalex.org/W4230288249","https://openalex.org/W6830866386"],"related_works":["https://openalex.org/W2356229341","https://openalex.org/W2349768204","https://openalex.org/W4313326281","https://openalex.org/W574867512","https://openalex.org/W2387271333","https://openalex.org/W581389233","https://openalex.org/W2361120309","https://openalex.org/W2387981414","https://openalex.org/W2361546210","https://openalex.org/W381115453"],"abstract_inverted_index":{"The":[0,16,49],"web":[1,51],"server":[2,52],"follows":[3],"a":[4],"client-server":[5],"architecture":[6],"built":[7],"on":[8,21],"PHP":[9],"and":[10,12,24,42],"HTML":[11],"utilizes":[13],"DelPhi":[14,50],"software.":[15],"computation":[17],"is":[18,53],"carried":[19],"out":[20],"supercomputer":[22],"cluster":[23],"results":[25],"are":[26],"given":[27],"back":[28],"to":[29,38],"the":[30,36,40],"user":[31],"via":[32,46],"http":[33],"protocol,":[34],"including":[35],"ability":[37],"visualize":[39],"structure":[41],"corresponding":[43],"electrostatic":[44],"potential":[45],"Jmol":[47],"implementation.":[48],"available":[54],"from":[55],"http://compbio.clemson.edu/delphi_webserver.":[56]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
