{"id":"https://openalex.org/W2119288062","doi":"https://doi.org/10.1093/bioinformatics/btm481","title":"Four-Body Scoring Function for Mutagenesis","display_name":"Four-Body Scoring Function for Mutagenesis","publication_year":2007,"publication_date":"2007-10-05","ids":{"openalex":"https://openalex.org/W2119288062","doi":"https://doi.org/10.1093/bioinformatics/btm481","mag":"2119288062","pmid":"https://pubmed.ncbi.nlm.nih.gov/17921497"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm481","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm481","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/22/3009/49857468/bioinformatics_23_22_3009.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/23/22/3009/49857468/bioinformatics_23_22_3009.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049067084","display_name":"Chris Deutsch","orcid":null},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Deutsch","raw_affiliation_strings":["Department of Mathematics, Washington State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Washington State University, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102955818","display_name":"Bala Krishnamoorthy","orcid":"https://orcid.org/0000-0002-2727-6547"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bala Krishnamoorthy","raw_affiliation_strings":["Department of Mathematics, Washington State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Washington State University, USA","institution_ids":["https://openalex.org/I72951846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3459,"has_fulltext":false,"cited_by_count":46,"citation_normalized_percentile":{"value":0.79882598,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"22","first_page":"3009","last_page":"3015"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9987000226974487,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/mutant","display_name":"Mutant","score":0.7174156904220581},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"Mutagenesis","score":0.6047919392585754},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5901110768318176},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.43817564845085144},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3845593333244324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3659880757331848},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34923055768013},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16771206259727478}],"concepts":[{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.7174156904220581},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.6047919392585754},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5901110768318176},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.43817564845085144},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3845593333244324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3659880757331848},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34923055768013},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16771206259727478}],"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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btm481","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm481","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/22/3009/49857468/bioinformatics_23_22_3009.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:17921497","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17921497","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:CiteSeerX.psu:10.1.1.559.7638","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.559.7638","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.math.wsu.edu/math/faculty/bkrishna/DT/Mutate/Final_FourBodyMutagenesis.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.99.1905","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.1905","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btm481v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm481","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm481","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/22/3009/49857468/bioinformatics_23_22_3009.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":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W269812687","https://openalex.org/W1508871633","https://openalex.org/W1517557846","https://openalex.org/W1553774094","https://openalex.org/W1569672130","https://openalex.org/W1589812083","https://openalex.org/W1967682948","https://openalex.org/W1974170352","https://openalex.org/W1975017420","https://openalex.org/W1976672938","https://openalex.org/W1985497496","https://openalex.org/W1994058693","https://openalex.org/W1996320633","https://openalex.org/W2001112839","https://openalex.org/W2004026586","https://openalex.org/W2017741040","https://openalex.org/W2019574765","https://openalex.org/W2021459325","https://openalex.org/W2029667189","https://openalex.org/W2035376403","https://openalex.org/W2040823078","https://openalex.org/W2050167630","https://openalex.org/W2054313195","https://openalex.org/W2056917387","https://openalex.org/W2065796798","https://openalex.org/W2072822306","https://openalex.org/W2074503341","https://openalex.org/W2087388427","https://openalex.org/W2091210419","https://openalex.org/W2092387745","https://openalex.org/W2097455735","https://openalex.org/W2099672241","https://openalex.org/W2103468069","https://openalex.org/W2116846654","https://openalex.org/W2118064616","https://openalex.org/W2121150070","https://openalex.org/W2121519777","https://openalex.org/W2130179054","https://openalex.org/W2130459941","https://openalex.org/W2136676634","https://openalex.org/W2142115754","https://openalex.org/W2145644903","https://openalex.org/W2148734380","https://openalex.org/W2172129621","https://openalex.org/W6630218964","https://openalex.org/W6648457236","https://openalex.org/W6669090329","https://openalex.org/W6673528498"],"related_works":["https://openalex.org/W2377600730","https://openalex.org/W2387405353","https://openalex.org/W2050054436","https://openalex.org/W2352453461","https://openalex.org/W2128665526","https://openalex.org/W2417618367","https://openalex.org/W2225940343","https://openalex.org/W4240785775","https://openalex.org/W2027223071","https://openalex.org/W2009647017"],"abstract_inverted_index":{"MOTIVATION:":[0],"There":[1],"is":[2],"a":[3,29,39,67,107,195,207,230,234],"need":[4],"for":[5,60,188],"an":[6,168,185],"efficient":[7,186],"and":[8,18,24,35,55,79,85,114,140,236],"accurate":[9],"computational":[10],"method":[11,30,187],"to":[12,47,73,130,143,221],"identify":[13],"the":[14,22,51,75,83,128,131,141,144,154,158,179],"effects":[15,76],"of":[16,26,62,77,87,96,111,133,136,146,149,174,192,194,206,216],"single-":[17,78,113],"multiple-residue":[19,80,115],"mutations":[20,81,98],"on":[21,82,94,233],"stability":[23,84,132],"reactivity":[25,86,145],"proteins.":[27,88],"Such":[28],"should":[31,44],"ideally":[32],"be":[33,45],"consistent":[34],"yet":[36],"applicable":[37],"in":[38,160],"widespread":[40],"manner,":[41],"i.e.":[42],"it":[43],"applied":[46],"various":[48],"proteins":[49],"under":[50],"same":[52],"parameter":[53],"settings,":[54],"have":[56],"good":[57],"predictive":[58],"power":[59],"all":[61,222,237],"them.":[63],"RESULTS:":[64],"We":[65,89,104,182],"develop":[66,184],"Delaunay":[68],"tessellation-based":[69],"four-body":[70,123,180],"scoring":[71,92,124],"function":[72,93,125],"predict":[74],"test":[90],"our":[91],"sets":[95],"single-point":[97],"used":[99],"by":[100,247],"several":[101],"previous":[102],"studies.":[103],"also":[105,183],"assemble":[106],"new,":[108],"diverse":[109],"set":[110],"237":[112],"mutations,":[116],"from":[117],"over":[118],"24":[119],"different":[120],"publications.":[121],"The":[122],"correctly":[126,243],"predicted":[127],"changes":[129,142,159],"169":[134],"out":[135,148],"210":[137],"mutants":[138,151,155,193,205,240],"(80.5%),":[139],"17":[147],"27":[150],"(63%).":[152],"For":[153],"that":[156],"had":[157],"stability/reactivity":[161],"quantified":[162],"(using":[163],"reaction":[164],"rates,":[165],"temperatures,":[166],"etc.),":[167],"average":[169],"Spearman":[170],"rank":[171],"correlation":[172],"coefficient":[173],"0.67":[175],"was":[176],"achieved":[177],"with":[178,214],"scores.":[181],"screening":[189],"huge":[190],"numbers":[191],"protein,":[196],"called":[197],"combinatorial":[198,248],"mutagenesis.":[199,249],"In":[200],"one":[201],"study,":[202],"64":[203],"million":[204],"cold-shock":[208],"nucleus":[209],"binding":[210],"domain":[211],"protein":[212],"1CSQ,":[213],"six":[215],"its":[217],"residues":[218],"being":[219],"changed":[220],"possible":[223],"(20)":[224],"amino":[225],"acids,":[226],"were":[227,242],"screened":[228],"within":[229],"few":[231],"hours":[232],"PC,":[235],"five":[238],"stabilizing":[239,246],"reported":[241],"identified":[244],"as":[245]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}