{"id":"https://openalex.org/W1976555399","doi":"https://doi.org/10.1093/nar/gkh394","title":"SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins","display_name":"SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins","publication_year":2004,"publication_date":"2004-07-01","ids":{"openalex":"https://openalex.org/W1976555399","doi":"https://doi.org/10.1093/nar/gkh394","mag":"1976555399","pmid":"https://pubmed.ncbi.nlm.nih.gov/15215410"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkh394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh394","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W356/6208873/gkh394.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","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/nar/article-pdf/32/suppl_2/W356/6208873/gkh394.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050351424","display_name":"Lesheng Kong","orcid":"https://orcid.org/0000-0002-9225-3421"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"L. Kong","raw_affiliation_strings":["Department of Biochemistry, National University of Singapore, 8 Medical Drive, 117597, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, National University of Singapore, 8 Medical Drive, 117597, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089089022","display_name":"B. T. K. Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"B. T. K. Lee","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108222100","display_name":"J. Tong","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"J. C. Tong","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108317608","display_name":"Tin Wee Tan","orcid":"https://orcid.org/0009-0008-7829-3647"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"T. W. Tan","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083278600","display_name":"Shoba Ranganathan","orcid":"https://orcid.org/0000-0002-8290-813X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. Ranganathan","raw_affiliation_strings":["Department of Molecular Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Sciences","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5050351424"],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":0.8442,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.69380009,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"32","issue":"Web Server","first_page":"W356","last_page":"W359"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T12827","display_name":"Biochemical and Molecular Research","score":0.9983999729156494,"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/template","display_name":"Template","score":0.6595927476882935},{"id":"https://openalex.org/keywords/personalization","display_name":"Personalization","score":0.5663991570472717},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5558369159698486},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5504251718521118},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.541546642780304},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5075889825820923},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4785462021827698},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.47029992938041687},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.45644858479499817},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.44658568501472473},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34337636828422546},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.26511797308921814},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17623034119606018},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13952693343162537},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.13162663578987122}],"concepts":[{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.6595927476882935},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.5663991570472717},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5558369159698486},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5504251718521118},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.541546642780304},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5075889825820923},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4785462021827698},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.47029992938041687},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.45644858479499817},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.44658568501472473},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34337636828422546},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.26511797308921814},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17623034119606018},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13952693343162537},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.13162663578987122},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C55352822","wikidata":"https://www.wikidata.org/wiki/Q5558978","display_name":"Gibbs isotherm","level":3,"score":0.0},{"id":"https://openalex.org/C58226133","wikidata":"https://www.wikidata.org/wiki/Q1324199","display_name":"Pulmonary surfactant","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020916","descriptor_name":"Conotoxins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020916","descriptor_name":"Conotoxins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020916","descriptor_name":"Conotoxins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkh394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh394","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W356/6208873/gkh394.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15215410","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15215410","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/38218","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/38218","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.104.5473","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.104.5473","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/reprint/32/suppl_2/W356.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:162769","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC441532","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:441532","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/441532","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkh394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh394","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_2/W356/6208873/gkh394.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320698","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1869944834","https://openalex.org/W1967194316","https://openalex.org/W1992155274","https://openalex.org/W2005008560","https://openalex.org/W2040000388","https://openalex.org/W2046060532","https://openalex.org/W2055925492","https://openalex.org/W2065283382","https://openalex.org/W2085277871","https://openalex.org/W2114520383","https://openalex.org/W2120107794","https://openalex.org/W2130479394","https://openalex.org/W2149480059","https://openalex.org/W2153582608","https://openalex.org/W2154320306"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W4234406076","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W2010731026","https://openalex.org/W2360893094","https://openalex.org/W4390787808","https://openalex.org/W4236036386","https://openalex.org/W4231091074"],"abstract_inverted_index":{"Small":[0],"disulfide-bonded":[1],"proteins":[2,14],"(SDPs)":[3],"are":[4],"rich":[5],"sources":[6],"for":[7,23],"therapeutic":[8],"drugs.":[9],"Designing":[10],"drugs":[11],"from":[12,78],"these":[13,27],"requires":[15],"three-dimensional":[16],"structural":[17,34],"information,":[18],"which":[19],"is":[20,114],"only":[21],"available":[22,40],"a":[24,38,54,62,68,79],"subset":[25],"of":[26,61,85,98],"proteins.":[28],"SDPMOD":[29,52,113],"addresses":[30],"this":[31],"deficit":[32],"in":[33],"information":[35],"by":[36],"providing":[37],"freely":[39,115],"automated":[41],"comparative":[42],"modeling":[43,100],"service":[44,105],"to":[45,74,117],"the":[46,59,76,83,91,99,103,121],"research":[47],"community.":[48],"For":[49],"expert":[50,87],"users,":[51],"offers":[53],"manual":[55],"mode":[56,70],"that":[57,71],"permits":[58],"selection":[60,84],"desired":[63],"template":[64,77],"as":[65,67],"well":[66],"semi-automated":[69],"allows":[72],"users":[73,88,119],"select":[75],"suggested":[80],"list.":[81],"Besides":[82],"templates,":[86],"can":[89],"edit":[90],"target-template":[92],"alignment,":[93],"thus":[94],"allowing":[95],"further":[96],"customization":[97],"process.":[101],"Furthermore,":[102],"web":[104,122],"provides":[106],"model":[107],"stereochemical":[108],"quality":[109],"evaluation":[110],"using":[111],"PROCHECK.":[112],"accessible":[116],"academic":[118],"via":[120],"interface":[123],"at":[124],"http://proline.bic.nus.edu.sg/sdpmod.":[125]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}