{"id":"https://openalex.org/W2174436514","doi":"https://doi.org/10.1021/ci050473v","title":"In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic \u03b1-Amylases upon Exhaustive Single-Site Mutations","display_name":"In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic \u03b1-Amylases upon Exhaustive Single-Site Mutations","publication_year":2006,"publication_date":"2006-02-18","ids":{"openalex":"https://openalex.org/W2174436514","doi":"https://doi.org/10.1021/ci050473v","mag":"2174436514","pmid":"https://pubmed.ncbi.nlm.nih.gov/16711770"},"language":"en","primary_location":{"id":"doi:10.1021/ci050473v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci050473v","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5068948301","display_name":"Dimitri Gilis","orcid":"https://orcid.org/0000-0001-9009-9996"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Dimitri Gilis","raw_affiliation_strings":["Genomic and Structural Bioinformatics, Universit\u00e9 Libre de Bruxelles, Avenue F. Roosevelt 50 CP 165/61, 1050 Brussels, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomic and Structural Bioinformatics, Universit\u00e9 Libre de Bruxelles, Avenue F. Roosevelt 50 CP 165/61, 1050 Brussels, Belgium","institution_ids":["https://openalex.org/I132053463"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5068948301"],"corresponding_institution_ids":["https://openalex.org/I132053463"],"apc_list":null,"apc_paid":null,"fwci":0.6023,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.71511277,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"46","issue":"3","first_page":"1509","last_page":"1516"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11617","display_name":"Enzyme Production and Characterization","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/T11617","display_name":"Enzyme Production and Characterization","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12827","display_name":"Biochemical and Molecular Research","score":0.9944000244140625,"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/psychrophile","display_name":"Psychrophile","score":0.9791423678398132},{"id":"https://openalex.org/keywords/mesophile","display_name":"Mesophile","score":0.7913104891777039},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7448617219924927},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5950564742088318},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4880744218826294},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4400116801261902},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.43056654930114746},{"id":"https://openalex.org/keywords/chemical-stability","display_name":"Chemical stability","score":0.4282371401786804},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39367568492889404},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3901962637901306},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37836578488349915},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11829423904418945},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.06979000568389893}],"concepts":[{"id":"https://openalex.org/C22802001","wikidata":"https://www.wikidata.org/wiki/Q913343","display_name":"Psychrophile","level":3,"score":0.9791423678398132},{"id":"https://openalex.org/C63223902","wikidata":"https://www.wikidata.org/wiki/Q669652","display_name":"Mesophile","level":3,"score":0.7913104891777039},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7448617219924927},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5950564742088318},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4880744218826294},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4400116801261902},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.43056654930114746},{"id":"https://openalex.org/C186399102","wikidata":"https://www.wikidata.org/wiki/Q903517","display_name":"Chemical stability","level":2,"score":0.4282371401786804},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39367568492889404},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3901962637901306},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37836578488349915},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11829423904418945},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.06979000568389893},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000516","descriptor_name":"alpha-Amylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D013552","descriptor_name":"Swine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013552","descriptor_name":"Swine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013552","descriptor_name":"Swine","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":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci050473v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci050473v","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:16711770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16711770","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:dipot.ulb.ac.be:2013/60559","is_oa":false,"landing_page_url":"https://dipot.ulb.ac.be/dspace/bitstream/2013/60559/1/2006_Gilis_JChemInfoModel.pdf","pdf_url":"https://dipot.ulb.ac.be/dspace/bitstream/2013/60559/1/2006_Gilis_JChemInfoModel.pdf","source":{"id":"https://openalex.org/S4306401063","display_name":"D\u00e9p\u00f4t institutionnel de l'Universit\u00e9 libre de Bruxelles (Universit\u00e9 Libre de Bruxelles)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I132053463","host_organization_name":"Universit\u00e9 Libre de Bruxelles","host_organization_lineage":["https://openalex.org/I132053463"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of chemical information and modeling, 46 (3","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321584","display_name":"F\u00e9d\u00e9ration Wallonie-Bruxelles","ror":"https://ror.org/04q01pf08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W174651672","https://openalex.org/W1591716364","https://openalex.org/W1966190762","https://openalex.org/W1980457410","https://openalex.org/W1980526190","https://openalex.org/W1988883176","https://openalex.org/W1995730663","https://openalex.org/W1998041471","https://openalex.org/W1998902553","https://openalex.org/W2004635124","https://openalex.org/W2006425558","https://openalex.org/W2008913755","https://openalex.org/W2020248033","https://openalex.org/W2033809613","https://openalex.org/W2065837861","https://openalex.org/W2066332174","https://openalex.org/W2075031865","https://openalex.org/W2078717114","https://openalex.org/W2080117472","https://openalex.org/W2087293973","https://openalex.org/W2090778342","https://openalex.org/W2090799488","https://openalex.org/W2093969953","https://openalex.org/W2100494857","https://openalex.org/W2106882534","https://openalex.org/W2107059140","https://openalex.org/W2108067237","https://openalex.org/W2110958200","https://openalex.org/W2122631536","https://openalex.org/W2127670645","https://openalex.org/W2130479394","https://openalex.org/W2136447744","https://openalex.org/W2147864921","https://openalex.org/W2151687360","https://openalex.org/W2154346441","https://openalex.org/W2157826157","https://openalex.org/W2158543301","https://openalex.org/W2159687889","https://openalex.org/W2161579403","https://openalex.org/W2163878108","https://openalex.org/W2168568729","https://openalex.org/W2170644505","https://openalex.org/W2171741848","https://openalex.org/W2312677902","https://openalex.org/W4251769520"],"related_works":["https://openalex.org/W2112448246","https://openalex.org/W2008467184","https://openalex.org/W2468935073","https://openalex.org/W4308800371","https://openalex.org/W2082704346","https://openalex.org/W2599806902","https://openalex.org/W2088998327","https://openalex.org/W1981086489","https://openalex.org/W2316964325","https://openalex.org/W4239172529"],"abstract_inverted_index":{"Identifying":[0],"sequence":[1,60],"modifications":[2],"that":[3,62,115,151],"distinguish":[4],"psychrophilic":[5,42,77,87,127,158],"from":[6],"mesophilic":[7,39,79,99],"proteins":[8,100],"is":[9,27],"important":[10],"for":[11,122],"designing":[12],"enzymes":[13],"with":[14,135,175,180],"different":[15],"thermodynamic":[16,51,161,197],"stabilities":[17],"and":[18,40,45,78,94],"to":[19,29,46,97,131,146,154,156],"understand":[20],"the":[21,34,48,56,59,73,83,86,98,107,112,116,123,126,139,157,166,173,184,196,200,207],"underlying":[22],"mechanisms.":[23],"The":[24,53],"PoPMuSiC":[25],"algorithm":[26],"used":[28],"introduce,":[30],"in":[31,37,50,91,106,169,178,213],"silico,":[32],"all":[33],"single-site":[35,194],"mutations":[36,84,150,167,202],"four":[38],"one":[41],"chloride-dependent":[43],"alpha-amylases":[44],"evaluate":[47],"changes":[49],"stability.":[52],"analysis":[54],"of":[55,58,76,82,118,125,165,186,199],"distribution":[57],"positions":[61],"could":[63],"be":[64,204],"stabilized":[65],"upon":[66],"mutation":[67],"shows":[68],"a":[69],"clear":[70],"difference":[71],"between":[72],"three":[74],"domains":[75,92],"alpha-amylases.":[80],"Most":[81],"stabilizing":[85],"enzyme":[88,159],"are":[89,103,144,152,210],"found":[90,168],"B":[93],"C,":[95],"contrary":[96],"where":[101],"they":[102],"preferentially":[104],"situated":[105],"catalytic":[108],"domain":[109,170,176],"A.":[110],"Moreover,":[111],"calculations":[113],"show":[114],"environment":[117],"some":[119],"residues":[120,209],"responsible":[121],"activity":[124],"protein":[128],"has":[129],"evolved":[130],"reinforce":[132],"favorable":[133],"interactions":[134,174],"these":[136,142],"residues.":[137],"In":[138],"second":[140],"part,":[141],"results":[143],"exploited":[145],"propose":[147],"rationally":[148],"designed":[149],"predicted":[153],"confer":[155],"mesophilic-like":[160],"properties.":[162],"Interestingly,":[163],"most":[164],"C":[171],"strengthen":[172],"A,":[177],"agreement":[179],"suggestions":[181],"made":[182],"on":[183,193],"basis":[185],"structural":[187],"analyses.":[188],"Although":[189],"this":[190],"study":[191],"focuses":[192],"mutations,":[195],"effects":[198],"recommended":[201],"should":[203],"additive":[205],"if":[206],"mutated":[208],"not":[211],"close":[212],"space.":[214]},"counts_by_year":[],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2016-06-24T00:00:00"}