{"id":"https://openalex.org/W2085429804","doi":"https://doi.org/10.1093/nar/gks488","title":"CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods","display_name":"CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods","publication_year":2012,"publication_date":"2012-06-04","ids":{"openalex":"https://openalex.org/W2085429804","doi":"https://doi.org/10.1093/nar/gks488","mag":"2085429804","pmid":"https://pubmed.ncbi.nlm.nih.gov/22669913"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gks488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks488","pdf_url":"https://academic.oup.com/nar/article-pdf/40/W1/W329/4926234/gks488.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":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/40/W1/W329/4926234/gks488.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028914297","display_name":"D\u00e1niel Kozma","orcid":"https://orcid.org/0000-0002-7334-0546"},"institutions":[{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"funder","lineage":["https://openalex.org/I7597260"]},{"id":"https://openalex.org/I4210151515","display_name":"Institute of Molecular Life Sciences","ror":"https://ror.org/04t4pws42","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210151515","https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"D. Kozma","raw_affiliation_strings":["Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary","Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary","institution_ids":["https://openalex.org/I80251312","https://openalex.org/I7597260","https://openalex.org/I4210151515"]},{"raw_affiliation_string":"Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary","institution_ids":["https://openalex.org/I80251312","https://openalex.org/I7597260","https://openalex.org/I4210151515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078144452","display_name":"Istv\u00e1n Simon","orcid":"https://orcid.org/0000-0003-1207-4018"},"institutions":[{"id":"https://openalex.org/I4210151515","display_name":"Institute of Molecular Life Sciences","ror":"https://ror.org/04t4pws42","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210151515","https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"funder","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"I. Simon","raw_affiliation_strings":["Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary","institution_ids":["https://openalex.org/I80251312","https://openalex.org/I7597260","https://openalex.org/I4210151515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025649527","display_name":"G\u00e1bor Tusn\u00e1dy","orcid":"https://orcid.org/0000-0001-8105-0285"},"institutions":[{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"funder","lineage":["https://openalex.org/I7597260"]},{"id":"https://openalex.org/I4210151515","display_name":"Institute of Molecular Life Sciences","ror":"https://ror.org/04t4pws42","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210151515","https://openalex.org/I4387152226","https://openalex.org/I80251312"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"G. E. Tusnady","raw_affiliation_strings":["Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 7,H-1518 Budapest, Hungary","institution_ids":["https://openalex.org/I80251312","https://openalex.org/I7597260","https://openalex.org/I4210151515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028914297"],"corresponding_institution_ids":["https://openalex.org/I4210151515","https://openalex.org/I7597260","https://openalex.org/I80251312"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.9412,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.74049451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"40","issue":"W1","first_page":"W329","last_page":"W333"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9994000196456909,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9922000169754028,"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/web-server","display_name":"Web server","score":0.6204019784927368},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.567827582359314},{"id":"https://openalex.org/keywords/web-browser","display_name":"Web browser","score":0.5570305585861206},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.5168929100036621},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5059849619865417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4936321973800659},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.33391714096069336},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32581859827041626},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2070375680923462},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.1308443546295166}],"concepts":[{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6204019784927368},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.567827582359314},{"id":"https://openalex.org/C2983909278","wikidata":"https://www.wikidata.org/wiki/Q6368","display_name":"Web browser","level":3,"score":0.5570305585861206},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.5168929100036621},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5059849619865417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4936321973800659},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.33391714096069336},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32581859827041626},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2070375680923462},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.1308443546295166}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gks488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks488","pdf_url":"https://academic.oup.com/nar/article-pdf/40/W1/W329/4926234/gks488.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":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22669913","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22669913","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:europepmc.org:2409800","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3394325","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":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/W1/W329","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/W1/W329","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gks488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks488","pdf_url":"https://academic.oup.com/nar/article-pdf/40/W1/W329/4926234/gks488.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":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8988120703","display_name":null,"funder_award_id":"NK100482","funder_id":"https://openalex.org/F4320321994","funder_display_name":"Hungarian Scientific Research Fund"}],"funders":[{"id":"https://openalex.org/F4320321994","display_name":"Hungarian Scientific Research Fund","ror":"https://ror.org/00v349e63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2085429804.pdf","grobid_xml":"https://content.openalex.org/works/W2085429804.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1572961809","https://openalex.org/W1994983243","https://openalex.org/W2087300028","https://openalex.org/W2092006899","https://openalex.org/W2094657451","https://openalex.org/W2097980499","https://openalex.org/W2100063856","https://openalex.org/W2120549641","https://openalex.org/W2122414179","https://openalex.org/W2128044898","https://openalex.org/W2129838159","https://openalex.org/W2141366228","https://openalex.org/W2144152753","https://openalex.org/W2166701319","https://openalex.org/W2168904132","https://openalex.org/W2171641243"],"related_works":["https://openalex.org/W2944823289","https://openalex.org/W3037018281","https://openalex.org/W2972592048","https://openalex.org/W2358319515","https://openalex.org/W4321854979","https://openalex.org/W4234342421","https://openalex.org/W2909040123","https://openalex.org/W2084305201","https://openalex.org/W2033854691","https://openalex.org/W2380066699"],"abstract_inverted_index":{"A":[0],"contact":[1,49,64,67,91,121,138,145],"map":[2],"is":[3,51,164,179,185,189],"a":[4,152,166,175],"2D":[5],"derivative":[6],"of":[7,11,29,48,63,142,161],"the":[8,19,27,39,45,125,130,156],"3D":[9,102],"structure":[10,30,57],"proteins,":[12],"containing":[13],"various":[14,46,112],"residue-residue":[15],"(RR)":[16],"contacts":[17,95,135],"within":[18],"structure.":[20],"Contact":[21,76],"maps":[22,50],"can":[23,35,86,148],"be":[24,36,87,149],"used":[25,88],"for":[26,82,170],"reconstruction":[28],"with":[31],"high":[32],"accuracy":[33],"and":[34,66,96,104,109,132],"predicted":[37,131],"from":[38],"amino":[40],"acid":[41],"sequence.":[42],"Therefore":[43],"understanding":[44],"properties":[47,62],"an":[52,72],"important":[53],"step":[54],"in":[55,101,105,124,136],"protein":[56],"prediction.":[58],"For":[59],"investigating":[60],"basic":[61],"formation":[65],"clusters":[68],"we":[69,117],"set":[70],"up":[71],"integrated":[73],"system":[74],"called":[75],"Map":[77],"Web":[78],"Viewer,":[79],"or":[80],"CMWeb":[81,126,188],"short.":[83],"The":[84,140,187],"server":[85,127,157],"to":[89,93,97,110,128],"visualize":[90,129],"maps,":[92],"link":[94],"show":[98],"them":[99],"both":[100],"structures":[103],"multiple":[106],"sequence":[107],"alignments":[108],"calculate":[111],"statistics":[113],"on":[114],"contacts.":[115],"Moreover,":[116],"have":[118],"implemented":[119],"five":[120],"prediction":[122,146],"methods":[123,147],"real":[133],"RR":[134,144],"one":[137],"map.":[139],"results":[141],"other":[143],"uploaded":[150],"as":[151,158],"benchmark":[153],"test":[154],"onto":[155],"well.":[159],"All":[160],"these":[162],"functionality":[163],"behind":[165],"web":[167,177],"server,":[168],"thus":[169],"using":[171],"our":[172],"application":[173],"only":[174],"Java-capable":[176],"browser":[178],"needed,":[180],"no":[181],"further":[182],"program":[183],"installation":[184],"required.":[186],"freely":[190],"accessible":[191],"at":[192],"http://cmweb.enzim.hu.":[193]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
