{"id":"https://openalex.org/W2998716839","doi":"https://doi.org/10.1093/bib/bbz168","title":"On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation","display_name":"On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation","publication_year":2019,"publication_date":"2019-12-06","ids":{"openalex":"https://openalex.org/W2998716839","doi":"https://doi.org/10.1093/bib/bbz168","mag":"2998716839","pmid":"https://pubmed.ncbi.nlm.nih.gov/31885042"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz168","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz168","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/601/35934973/bbz168.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/22/1/601/35934973/bbz168.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069439283","display_name":"Castrense Savojardo","orcid":"https://orcid.org/0000-0002-7359-0633"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Castrense Savojardo","raw_affiliation_strings":["Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044479288","display_name":"Pier Luigi Martelli","orcid":"https://orcid.org/0000-0002-0274-5669"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Pier Luigi Martelli","raw_affiliation_strings":["Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053410790","display_name":"Rita Casadio","orcid":"https://orcid.org/0000-0002-7462-7039"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rita Casadio","raw_affiliation_strings":["Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060232841","display_name":"Piero Fariselli","orcid":"https://orcid.org/0000-0003-1811-4762"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Piero Fariselli","raw_affiliation_strings":["Department of Medical Sciences, University of Torino, Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Medical Sciences, University of Torino, Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044479288"],"corresponding_institution_ids":["https://openalex.org/I9360294"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.6848,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.70009799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"22","issue":"1","first_page":"601","last_page":"603"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.998199999332428,"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":0.998199999332428,"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":0.9927999973297119,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9922999739646912,"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/complement","display_name":"Complement (music)","score":0.7947533130645752},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.6647118330001831},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6516294479370117},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5959672927856445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5237236618995667},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5023112297058105},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.48870185017585754},{"id":"https://openalex.org/keywords/fang","display_name":"Fang","score":0.465924471616745},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.4611222445964813},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4255383312702179},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16236254572868347},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14408013224601746},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.11955147981643677},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08438378572463989},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06961992383003235}],"concepts":[{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.7947533130645752},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.6647118330001831},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6516294479370117},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5959672927856445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5237236618995667},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5023112297058105},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.48870185017585754},{"id":"https://openalex.org/C2778774319","wikidata":"https://www.wikidata.org/wiki/Q1940269","display_name":"Fang","level":2,"score":0.465924471616745},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.4611222445964813},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4255383312702179},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16236254572868347},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14408013224601746},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.11955147981643677},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08438378572463989},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06961992383003235},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbz168","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz168","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/601/35934973/bbz168.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31885042","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31885042","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:cris.unibo.it:11585/799910","is_oa":true,"landing_page_url":"https://hdl.handle.net/11585/799910","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbz168","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz168","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/601/35934973/bbz168.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G6389209724","display_name":null,"funder_award_id":"D15D18000410001","funder_id":"https://openalex.org/F4320317295","funder_display_name":"Dipartimenti di Eccellenza"}],"funders":[{"id":"https://openalex.org/F4320317295","display_name":"Dipartimenti di Eccellenza","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2998716839.pdf","grobid_xml":"https://content.openalex.org/works/W2998716839.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W2005756796","https://openalex.org/W2026932582","https://openalex.org/W2056053449","https://openalex.org/W2104418738","https://openalex.org/W2134488721","https://openalex.org/W2161690185","https://openalex.org/W2324374958","https://openalex.org/W2471400579","https://openalex.org/W2794503008","https://openalex.org/W2799513065","https://openalex.org/W2893067056","https://openalex.org/W2902559445","https://openalex.org/W2947281209","https://openalex.org/W2949829516","https://openalex.org/W2953906682","https://openalex.org/W2955704392","https://openalex.org/W2969598887","https://openalex.org/W6683903387","https://openalex.org/W6766500604"],"related_works":["https://openalex.org/W2373744651","https://openalex.org/W2390188116","https://openalex.org/W1578091436","https://openalex.org/W2356575882","https://openalex.org/W2361002015","https://openalex.org/W2418884610","https://openalex.org/W2365286095","https://openalex.org/W2390562971","https://openalex.org/W4393806872","https://openalex.org/W2291094979"],"abstract_inverted_index":{"A":[0],"review,":[1],"recently":[2],"published":[3,79],"in":[4,80],"this":[5,58],"journal":[6],"by":[7],"Fang":[8],"(2019),":[9],"showed":[10],"that":[11,30,97],"methods":[12],"trained":[13],"for":[14],"the":[15,45,49,62,71,84,90,93,103],"prediction":[16],"of":[17,48,70,92],"protein":[18,32],"stability":[19],"changes":[20],"upon":[21],"mutation":[22],"have":[23,44],"a":[24,31,66,75],"very":[25],"critical":[26],"bias:":[27],"they":[28],"neglect":[29],"variation":[33],"(A-":[34],">":[35,41],"B)":[36],"and":[37],"its":[38],"reverse":[39],"(B-":[40],"A)":[42],"must":[43],"opposite":[46],"value":[47],"free":[50],"energy":[51],"difference":[52],"(\u0394\u0394GAB":[53],"=":[54],"-":[55],"\u0394\u0394GBA).":[56],"In":[57,73],"letter,":[59],"we":[60],"complement":[61],"Fang's":[63],"paper":[64],"presenting":[65],"more":[67],"general":[68],"view":[69],"problem.":[72,105],"particular,":[74],"machine":[76],"learning-based":[77],"method,":[78,95],"2015":[81],"(INPS),":[82],"addressed":[83,104],"bias":[85],"issue":[86],"directly.":[87],"We":[88],"include":[89],"analysis":[91],"missing":[94],"showing":[96],"INPS":[98],"is":[99],"nearly":[100],"insensitive":[101],"to":[102]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
