{"id":"https://openalex.org/W2018076081","doi":"https://doi.org/10.1002/jcc.20700","title":"Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices","display_name":"Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices","publication_year":2007,"publication_date":"2007-04-20","ids":{"openalex":"https://openalex.org/W2018076081","doi":"https://doi.org/10.1002/jcc.20700","mag":"2018076081","pmid":"https://pubmed.ncbi.nlm.nih.gov/17450569"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.20700","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.20700","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013497733","display_name":"Humberto Gonz\u00e1lez\u2010D\u00edaz","orcid":"https://orcid.org/0000-0002-9392-2797"},"institutions":[{"id":"https://openalex.org/I172446870","display_name":"University of Cagliari","ror":"https://ror.org/003109y17","country_code":"IT","type":"education","lineage":["https://openalex.org/I172446870"]},{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]}],"countries":["ES","IT"],"is_corresponding":true,"raw_author_name":"Humberto Gonz\u00e1lez\u2010D\u00edaz","raw_affiliation_strings":["Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain. gonzalezdiazh@yahoo.es","Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain","Dipartimento Farmaco Chimico Tecnologico, Universit\u00e1 Degli Studi di Cagliari, Cagliari 09124, Italy"],"affiliations":[{"raw_affiliation_string":"Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain. gonzalezdiazh@yahoo.es","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain","institution_ids":["https://openalex.org/I200284239"]},{"raw_affiliation_string":"Dipartimento Farmaco Chimico Tecnologico, Universit\u00e1 Degli Studi di Cagliari, Cagliari 09124, Italy","institution_ids":["https://openalex.org/I172446870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040406602","display_name":"Yunierkis P\u00e9rez\u2010Castillo","orcid":"https://orcid.org/0000-0002-3710-0035"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Yunierkis P\u00e9rez\u2010castillo","raw_affiliation_strings":["Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain"],"affiliations":[{"raw_affiliation_string":"Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain","institution_ids":["https://openalex.org/I200284239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111753317","display_name":"Gianni Podda","orcid":null},"institutions":[{"id":"https://openalex.org/I172446870","display_name":"University of Cagliari","ror":"https://ror.org/003109y17","country_code":"IT","type":"education","lineage":["https://openalex.org/I172446870"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianni Podda","raw_affiliation_strings":["Dipartimento Farmaco Chimico Tecnologico, Universita\u0301 Degli Studi di Cagliari, Cagliari 09124, Italy","Dipartimento Farmaco Chimico Tecnologico, Universit\u00e1 Degli Studi di Cagliari, Cagliari 09124, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento Farmaco Chimico Tecnologico, Universita\u0301 Degli Studi di Cagliari, Cagliari 09124, Italy","institution_ids":["https://openalex.org/I172446870"]},{"raw_affiliation_string":"Dipartimento Farmaco Chimico Tecnologico, Universit\u00e1 Degli Studi di Cagliari, Cagliari 09124, Italy","institution_ids":["https://openalex.org/I172446870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070602119","display_name":"Eugenio Uriarte","orcid":"https://orcid.org/0000-0001-6218-2899"},"institutions":[{"id":"https://openalex.org/I200284239","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10","country_code":"ES","type":"education","lineage":["https://openalex.org/I200284239"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Eugenio Uriarte","raw_affiliation_strings":["Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain"],"affiliations":[{"raw_affiliation_string":"Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain","institution_ids":["https://openalex.org/I200284239"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5013497733"],"corresponding_institution_ids":["https://openalex.org/I172446870","https://openalex.org/I200284239"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":4.712,"has_fulltext":false,"cited_by_count":61,"citation_normalized_percentile":{"value":0.95854562,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"28","issue":"12","first_page":"1990","last_page":"1995"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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"}}],"keywords":[{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.6463749408721924},{"id":"https://openalex.org/keywords/simplicity","display_name":"Simplicity","score":0.5374956727027893},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5367603898048401},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5206146240234375},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.46987348794937134},{"id":"https://openalex.org/keywords/protein-stability","display_name":"Protein stability","score":0.42674893140792847},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42518073320388794},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.41451483964920044},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38218626379966736},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3233022689819336},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25000208616256714},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.23878899216651917},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23632201552391052},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14600861072540283},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14554733037948608},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10749757289886475},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10177847743034363}],"concepts":[{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.6463749408721924},{"id":"https://openalex.org/C2776372474","wikidata":"https://www.wikidata.org/wiki/Q508291","display_name":"Simplicity","level":2,"score":0.5374956727027893},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5367603898048401},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5206146240234375},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.46987348794937134},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.42674893140792847},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42518073320388794},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.41451483964920044},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38218626379966736},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3233022689819336},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25000208616256714},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.23878899216651917},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23632201552391052},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14600861072540283},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14554733037948608},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10749757289886475},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10177847743034363},{"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":true},{"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":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1002/jcc.20700","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.20700","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},{"id":"pmid:17450569","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17450569","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":"Journal of computational chemistry","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"},{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W147273853","https://openalex.org/W623814603","https://openalex.org/W1516720576","https://openalex.org/W1545231783","https://openalex.org/W1549949328","https://openalex.org/W1963733856","https://openalex.org/W1964823421","https://openalex.org/W1980266776","https://openalex.org/W1981803782","https://openalex.org/W1992681902","https://openalex.org/W1995808589","https://openalex.org/W2008489796","https://openalex.org/W2009526534","https://openalex.org/W2010708237","https://openalex.org/W2016949897","https://openalex.org/W2023703189","https://openalex.org/W2025046262","https://openalex.org/W2028597865","https://openalex.org/W2029827832","https://openalex.org/W2029865295","https://openalex.org/W2033043436","https://openalex.org/W2040693785","https://openalex.org/W2050034583","https://openalex.org/W2055334398","https://openalex.org/W2058286156","https://openalex.org/W2058556255","https://openalex.org/W2065767445","https://openalex.org/W2070972624","https://openalex.org/W2072995782","https://openalex.org/W2074146738","https://openalex.org/W2075898920","https://openalex.org/W2081393301","https://openalex.org/W2084446624","https://openalex.org/W2089985004","https://openalex.org/W2091490591","https://openalex.org/W2094719223","https://openalex.org/W2109982997","https://openalex.org/W2121128310","https://openalex.org/W2125508887","https://openalex.org/W2133335870","https://openalex.org/W2134403677","https://openalex.org/W2160979370","https://openalex.org/W2164412882","https://openalex.org/W2167772971","https://openalex.org/W2171490488","https://openalex.org/W2196876065","https://openalex.org/W2203679171","https://openalex.org/W2203756811","https://openalex.org/W2219114748","https://openalex.org/W2221809994","https://openalex.org/W2766967542","https://openalex.org/W2951657858"],"related_works":["https://openalex.org/W2368019753","https://openalex.org/W2333930193","https://openalex.org/W2737356002","https://openalex.org/W2246241526","https://openalex.org/W2374150061","https://openalex.org/W4301122218","https://openalex.org/W2081340182","https://openalex.org/W2369703001","https://openalex.org/W4387581414","https://openalex.org/W3104156022"],"abstract_inverted_index":{"In":[0,61,86],"principle,":[1],"there":[2],"are":[3,36,56],"different":[4],"protein":[5,18,52],"structural":[6],"parameters":[7,31,40],"that":[8],"can":[9],"be":[10,59],"used":[11],"in":[12,95,134,151,155],"computational":[13],"chemistry":[14],"studies":[15],"to":[16,21,58,76,84],"classify":[17],"mutants":[19],"according":[20,83],"thermal":[22],"stability":[23],"including:":[24],"sequence,":[25],"connectivity,":[26],"and":[27,54,68],"3D":[28,39,67,108,136],"descriptors.":[29],"Connectivity":[30],"(called":[32],"topological":[33],"indices,":[34],"TIs)":[35],"simpler":[37],"than":[38,143],"being":[41],"then":[42],"less":[43],"computationally":[44],"expensive.":[45],"However,":[46],"TIs":[47,69,120,144,147],"ignore":[48],"important":[49],"aspects":[50],"of":[51,66,79,81,93,115,126,157],"structure":[53],"hence":[55],"expected":[57],"inaccurate.":[60],"any":[62],"case,":[63],"a":[64,152],"comparison":[65],"has":[70],"not":[71],"been":[72],"reported":[73],"with":[74],"respect":[75],"the":[77,99],"power":[78],"discrimination":[80],"proteins":[82,118],"stability.":[85],"this":[87,96],"study,":[88],"we":[89],"compare":[90],"both":[91],"classes":[92],"indices":[94],"sense":[97],"by":[98],"first":[100],"time.":[101],"The":[102],"best":[103],"model":[104,121],"found,":[105],"based":[106],"on":[107],"spectral":[109],"moments":[110],"correctly":[111,122],"classified":[112,123],"507":[113],"out":[114,125],"525":[116,127],"(96.6%)":[117],"while":[119],"404":[124],"(77.0%)":[128],"proteins.":[129],"We":[130],"have":[131],"shown":[132],"that,":[133],"fact,":[135],"descriptor":[137],"models":[138],"gave":[139],"more":[140],"accurate":[141],"results":[142,150],"but":[145],"interestingly,":[146],"give":[148],"acceptable":[149],"timely":[153],"way":[154],"spite":[156],"their":[158],"simplicity.":[159]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
