{"id":"https://openalex.org/W2109766743","doi":"https://doi.org/10.1093/bioinformatics/btm637","title":"Predicting disulfide bond connectivity in proteins by correlated mutations analysis","display_name":"Predicting disulfide bond connectivity in proteins by correlated mutations analysis","publication_year":2008,"publication_date":"2008-01-18","ids":{"openalex":"https://openalex.org/W2109766743","doi":"https://doi.org/10.1093/bioinformatics/btm637","mag":"2109766743","pmid":"https://pubmed.ncbi.nlm.nih.gov/18203772"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm637","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/498/49044604/bioinformatics_24_4_498.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/24/4/498/49044604/bioinformatics_24_4_498.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031169990","display_name":"Rotem Rubinstein","orcid":"https://orcid.org/0000-0003-3657-5984"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rotem Rubinstein","raw_affiliation_strings":["Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 (USA)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 (USA)","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040379692","display_name":"Andr\u00e1s Fiser","orcid":"https://orcid.org/0000-0003-0085-5335"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andras Fiser","raw_affiliation_strings":["Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 (USA)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 (USA)","institution_ids":["https://openalex.org/I129975664"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5040379692"],"corresponding_institution_ids":["https://openalex.org/I129975664"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.5588,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.82232404,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"4","first_page":"498","last_page":"504"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9927999973297119,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9927999973297119,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9904999732971191,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9851999878883362,"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/cysteine","display_name":"Cysteine","score":0.8240233659744263},{"id":"https://openalex.org/keywords/disulfide-bond","display_name":"Disulfide bond","score":0.8212444186210632},{"id":"https://openalex.org/keywords/protein-disulfide-isomerase","display_name":"Protein disulfide-isomerase","score":0.5613885521888733},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5350545644760132},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.42059099674224854},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.22015458345413208},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08478587865829468},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.060829371213912964}],"concepts":[{"id":"https://openalex.org/C2779201268","wikidata":"https://www.wikidata.org/wiki/Q186474","display_name":"Cysteine","level":3,"score":0.8240233659744263},{"id":"https://openalex.org/C27256138","wikidata":"https://www.wikidata.org/wiki/Q1230226","display_name":"Disulfide bond","level":2,"score":0.8212444186210632},{"id":"https://openalex.org/C5098756","wikidata":"https://www.wikidata.org/wiki/Q1641611","display_name":"Protein disulfide-isomerase","level":3,"score":0.5613885521888733},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5350545644760132},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.42059099674224854},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.22015458345413208},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08478587865829468},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.060829371213912964}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010434","descriptor_name":"Pepsin A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010434","descriptor_name":"Pepsin A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010434","descriptor_name":"Pepsin A","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":"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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm637","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/498/49044604/bioinformatics_24_4_498.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:18203772","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18203772","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm637","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/498/49044604/bioinformatics_24_4_498.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/G1533567685","display_name":null,"funder_award_id":"HHSN266200400054C","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109766743.pdf","grobid_xml":"https://content.openalex.org/works/W2109766743.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W6853809","https://openalex.org/W1484903051","https://openalex.org/W1984615569","https://openalex.org/W2003127757","https://openalex.org/W2009904974","https://openalex.org/W2013257734","https://openalex.org/W2021769301","https://openalex.org/W2031901496","https://openalex.org/W2033806446","https://openalex.org/W2049370744","https://openalex.org/W2056553106","https://openalex.org/W2068047393","https://openalex.org/W2068802139","https://openalex.org/W2080694804","https://openalex.org/W2082569982","https://openalex.org/W2085277871","https://openalex.org/W2087300028","https://openalex.org/W2090168101","https://openalex.org/W2090338919","https://openalex.org/W2094559779","https://openalex.org/W2096525273","https://openalex.org/W2097150498","https://openalex.org/W2108746608","https://openalex.org/W2117524891","https://openalex.org/W2123696579","https://openalex.org/W2126817143","https://openalex.org/W2127699503","https://openalex.org/W2128667006","https://openalex.org/W2131604629","https://openalex.org/W2131963349","https://openalex.org/W2135500937","https://openalex.org/W2137575385","https://openalex.org/W2143441933","https://openalex.org/W2148853951","https://openalex.org/W2153306103","https://openalex.org/W2154026159","https://openalex.org/W2156125289","https://openalex.org/W2158714788","https://openalex.org/W2160338675","https://openalex.org/W2161788422","https://openalex.org/W2163526800","https://openalex.org/W2171641243","https://openalex.org/W4241265708","https://openalex.org/W4245543257","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1980452076","https://openalex.org/W1010202294","https://openalex.org/W4239258835","https://openalex.org/W3185489799","https://openalex.org/W184948381","https://openalex.org/W2120426137","https://openalex.org/W2509147843","https://openalex.org/W1998396817","https://openalex.org/W2381745644","https://openalex.org/W4246113651"],"abstract_inverted_index":{"MOTIVATION:":[0],"Prediction":[1],"of":[2,11,18,56,71,77,90,109,119,141],"disulfide":[3,20,45,57,72,97,114,135,153],"bond":[4,21,46,73,115,136],"connectivity":[5,74,137],"facilitates":[6],"structural":[7],"and":[8,53,59,82,123,144,151],"functional":[9],"annotation":[10],"proteins.":[12],"Previous":[13],"studies":[14],"suggest":[15],"that":[16,32,60,87,107,124],"cysteines":[17,126],"a":[19,24,30,110,113],"mutate":[22],"in":[23,37,41,88,100,112,128],"correlated":[25,34],"manner.":[26],"RESULTS:":[27],"We":[28,67],"developed":[29,133],"method":[31,131],"analyzes":[33],"mutation":[35],"patterns":[36,138],"multiple":[38],"sequence":[39],"alignments":[40],"order":[42],"to":[43],"predict":[44],"connectivity.":[47],"Proteins":[48],"with":[49,139,148],"known":[50],"experimental":[51],"structures":[52],"varying":[54],"numbers":[55],"bonds,":[58,154],"spanned":[61],"various":[62],"evolutionary":[63],"distances,":[64],"were":[65],"aligned.":[66],"observed":[68,86],"frequent":[69],"variation":[70],"within":[75],"members":[76],"the":[78,91,105,117],"same":[79],"protein":[80],"families,":[81],"it":[83],"was":[84],"also":[85],"99%":[89],"cases,":[92],"cysteine":[93,111,121],"pairs":[94],"forming":[95],"non-conserved":[96],"bonds":[98],"mutated":[99],"concert.":[101],"Our":[102],"data":[103],"support":[104],"notion":[106],"substitution":[108,118],"prompts":[116],"its":[120],"partner":[122],"oxidized":[125],"appear":[127],"pairs.":[129],"The":[130],"we":[132],"predicts":[134],"accuracies":[140],"73,":[142],"69":[143],"61%":[145],"for":[146],"proteins":[147],"two,":[149],"three":[150],"four":[152],"respectively.":[155]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
