{"id":"https://openalex.org/W2890783151","doi":"https://doi.org/10.1093/bioinformatics/bty569","title":"Analysis of single amino acid variations in singlet hot spots of protein\u2013protein interfaces","display_name":"Analysis of single amino acid variations in singlet hot spots of protein\u2013protein interfaces","publication_year":2018,"publication_date":"2018-07-07","ids":{"openalex":"https://openalex.org/W2890783151","doi":"https://doi.org/10.1093/bioinformatics/bty569","mag":"2890783151","pmid":"https://pubmed.ncbi.nlm.nih.gov/30423104"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty569","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i795/25702610/bty569.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/34/17/i795/25702610/bty569.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103090077","display_name":"E. S\u0131la \u00d6zdemir","orcid":"https://orcid.org/0000-0003-0046-0667"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"E Sila Ozdemir","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036278069","display_name":"Attila G\u00fcrsoy","orcid":"https://orcid.org/0000-0002-2297-2113"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Attila Gursoy","raw_affiliation_strings":["Department of Computer Engineering, Koc University, Istanbul, Turkey","Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Koc University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057115991","display_name":"\u00d6zlem Keskin","orcid":"https://orcid.org/0000-0002-4202-4049"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Ozlem Keskin","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey","Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036278069","https://openalex.org/A5057115991"],"corresponding_institution_ids":["https://openalex.org/I1351752"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2058,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.79206725,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"17","first_page":"i795","last_page":"i801"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.855400025844574,"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":0.855400025844574,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.01679999940097332,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.013000000268220901,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hot-spot","display_name":"Hot spot (computer programming)","score":0.8062880039215088},{"id":"https://openalex.org/keywords/singlet-state","display_name":"Singlet state","score":0.6944065093994141},{"id":"https://openalex.org/keywords/amino-acid-residue","display_name":"Amino acid residue","score":0.6382541656494141},{"id":"https://openalex.org/keywords/spots","display_name":"Spots","score":0.5731619000434875},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.4634862244129181},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40345460176467896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3651772141456604},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3250824809074402},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.32034045457839966},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23413875699043274},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.208481103181839},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1787395179271698},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.09573769569396973},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.07986146211624146}],"concepts":[{"id":"https://openalex.org/C199672914","wikidata":"https://www.wikidata.org/wiki/Q4241353","display_name":"Hot spot (computer programming)","level":2,"score":0.8062880039215088},{"id":"https://openalex.org/C33062035","wikidata":"https://www.wikidata.org/wiki/Q3296863","display_name":"Singlet state","level":3,"score":0.6944065093994141},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.6382541656494141},{"id":"https://openalex.org/C2781255879","wikidata":"https://www.wikidata.org/wiki/Q7580087","display_name":"Spots","level":2,"score":0.5731619000434875},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.4634862244129181},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40345460176467896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3651772141456604},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3250824809074402},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.32034045457839966},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23413875699043274},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.208481103181839},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1787395179271698},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.09573769569396973},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.07986146211624146},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C181500209","wikidata":"https://www.wikidata.org/wiki/Q215328","display_name":"Excited state","level":2,"score":0.0}],"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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty569","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i795/25702610/bty569.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:30423104","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30423104","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty569","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i795/25702610/bty569.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":[{"score":0.4300000071525574,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W761483293","https://openalex.org/W1563940013","https://openalex.org/W1935098740","https://openalex.org/W1971938921","https://openalex.org/W1974599488","https://openalex.org/W1979237722","https://openalex.org/W1988152696","https://openalex.org/W1989181256","https://openalex.org/W2002052142","https://openalex.org/W2012673284","https://openalex.org/W2017847830","https://openalex.org/W2031772330","https://openalex.org/W2031942960","https://openalex.org/W2037048830","https://openalex.org/W2042103448","https://openalex.org/W2051710717","https://openalex.org/W2058527555","https://openalex.org/W2059145105","https://openalex.org/W2079317986","https://openalex.org/W2080088737","https://openalex.org/W2087574732","https://openalex.org/W2098656855","https://openalex.org/W2108267147","https://openalex.org/W2112702439","https://openalex.org/W2115156437","https://openalex.org/W2115167726","https://openalex.org/W2118151336","https://openalex.org/W2119097398","https://openalex.org/W2126389097","https://openalex.org/W2129342422","https://openalex.org/W2129558039","https://openalex.org/W2130479394","https://openalex.org/W2134755636","https://openalex.org/W2136206140","https://openalex.org/W2141624700","https://openalex.org/W2146208101","https://openalex.org/W2150066952","https://openalex.org/W2153127576","https://openalex.org/W2155030096","https://openalex.org/W2157807259","https://openalex.org/W2158945625","https://openalex.org/W2192013059","https://openalex.org/W2205143086","https://openalex.org/W2317557275","https://openalex.org/W2331480251","https://openalex.org/W2341018731","https://openalex.org/W2402268683","https://openalex.org/W2558879065","https://openalex.org/W2604078450","https://openalex.org/W2953103783","https://openalex.org/W3025428150","https://openalex.org/W6633589378","https://openalex.org/W6752065168"],"related_works":["https://openalex.org/W1997967488","https://openalex.org/W2593833119","https://openalex.org/W2224840501","https://openalex.org/W2088052375","https://openalex.org/W3039575483","https://openalex.org/W4311446160","https://openalex.org/W2045240459","https://openalex.org/W2736580264","https://openalex.org/W2890783151","https://openalex.org/W2159291387"],"abstract_inverted_index":{"Motivation:":[0],"Single":[1],"amino":[2,49],"acid":[3,50],"variations":[4],"(SAVs)":[5],"in":[6,14,101,123,143,151,160,179],"protein-protein":[7],"interaction":[8],"(PPI)":[9],"sites":[10,17],"play":[11],"critical":[12],"roles":[13],"diseases.":[15],"PPI":[16,130],"(interfaces)":[18],"have":[19,165],"a":[20],"small":[21],"subset":[22],"of":[23,54,60,80],"residues":[24,65,119,164],"called":[25,40],"hot":[26,41,44,51,56,103,107,137,162],"spots":[27,45,52,104,138],"that":[28,90,135,158],"contribute":[29],"significantly":[30,121,149],"to":[31,69,98,140],"the":[32,47,55,63],"binding":[33],"energy,":[34],"and":[35,77,88,109,171,174],"they":[36],"may":[37,66],"form":[38],"clusters":[39],"regions.":[42,57],"Singlet":[43],"are":[46,95,120,200],"single":[48],"outside":[53],"The":[58,176,187],"distribution":[59],"SAVs":[61,81,91,148,159],"on":[62,168],"interface":[64,113],"be":[67,99,141,190],"related":[68],"their":[70],"disease":[71],"association.":[72],"Results:":[73],"We":[74],"performed":[75],"statistical":[76],"structural":[78],"analyses":[79],"with":[82],"literature":[83],"curated":[84],"experimental":[85],"thermodynamics":[86],"data,":[87],"demonstrated":[89],"which":[92,126],"destabilize":[93],"PPIs":[94],"more":[96],"likely":[97],"found":[100,191],"singlet":[102,136,161],"rather":[105],"than":[106],"regions":[108],"energetically":[110],"less":[111],"important":[112],"residues.":[114,154],"In":[115],"contrast,":[116],"non-hot":[117,152],"spot":[118,153,163],"enriched":[122,142],"neutral":[124],"SAVs,":[125,145],"do":[127],"not":[128],"affect":[129],"stability.":[131],"Surprisingly,":[132],"we":[133],"observed":[134],"tend":[139],"disease-causing":[144],"while":[146],"benign":[147],"occur":[150],"Our":[155],"work":[156],"demonstrates":[157],"significant":[166],"effect":[167],"protein":[169],"stability":[170],"function.":[172],"Availability":[173],"implementation:":[175],"dataset":[177],"used":[178],"this":[180],"paper":[181],"is":[182],"available":[183,201],"as":[184,194],"Supplementary":[185,196,198],"Material.":[186],"data":[188,199],"can":[189],"at":[192,202],"http://prism.ccbb.ku.edu.tr/data/sav/":[193],"well.":[195],"information:":[197],"Bioinformatics":[203],"online.":[204]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
