{"id":"https://openalex.org/W2118714546","doi":"https://doi.org/10.1093/nar/gkp410","title":"HotSpot Wizard: a web server for identification of hot spots in protein engineering","display_name":"HotSpot Wizard: a web server for identification of hot spots in protein engineering","publication_year":2009,"publication_date":"2009-05-21","ids":{"openalex":"https://openalex.org/W2118714546","doi":"https://doi.org/10.1093/nar/gkp410","mag":"2118714546","pmid":"https://pubmed.ncbi.nlm.nih.gov/19465397"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkp410","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp410","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W376/3951406/gkp410.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W376/3951406/gkp410.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037343661","display_name":"Anton\u00edn Pavelka","orcid":"https://orcid.org/0000-0003-0084-402X"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"A. Pavelka","raw_affiliation_strings":["Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082008412","display_name":"Eva Chovancov\u00e1","orcid":"https://orcid.org/0000-0001-8016-0837"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"E. Chovancova","raw_affiliation_strings":["Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040585952","display_name":"Ji\u0159\u0131\u0301 Damborsk\u00fd","orcid":"https://orcid.org/0000-0002-7848-8216"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"J. Damborsky","raw_affiliation_strings":["Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5040585952"],"corresponding_institution_ids":["https://openalex.org/I21449261"],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":{"value":3992,"currency":"USD","value_usd":3992},"fwci":3.1993,"has_fulltext":true,"cited_by_count":200,"citation_normalized_percentile":{"value":0.92368157,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"37","issue":"Web Server","first_page":"W376","last_page":"W383"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9969000220298767,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9969000220298767,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9952999949455261,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9934999942779541,"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/wizard","display_name":"Wizard","score":0.7068761587142944},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6866227388381958},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.5040425658226013},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.47270986437797546},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47162580490112305},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3567807674407959},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.316727876663208},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.26970112323760986},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23882195353507996},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.11308124661445618}],"concepts":[{"id":"https://openalex.org/C2776784076","wikidata":"https://www.wikidata.org/wiki/Q580334","display_name":"Wizard","level":2,"score":0.7068761587142944},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6866227388381958},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5040425658226013},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.47270986437797546},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47162580490112305},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3567807674407959},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.316727876663208},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.26970112323760986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23882195353507996},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.11308124661445618},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001618","descriptor_name":"beta-Lactamases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006026","descriptor_name":"Glycoside Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006026","descriptor_name":"Glycoside Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006026","descriptor_name":"Glycoside Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044345","descriptor_name":"Phosphoric Triester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D044345","descriptor_name":"Phosphoric Triester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D044345","descriptor_name":"Phosphoric Triester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkp410","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp410","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W376/3951406/gkp410.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:19465397","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19465397","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":"Nucleic acids research","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2703904","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2703904","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkp410","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp410","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W376/3951406/gkp410.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5546893007","display_name":null,"funder_award_id":"MSM 0021622412","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G7886260290","display_name":null,"funder_award_id":"LC06010","funder_id":"https://openalex.org/F4320322482","funder_display_name":"Akademie V\u011bd \u010cesk\u00e9 Republiky"}],"funders":[{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"},{"id":"https://openalex.org/F4320322482","display_name":"Akademie V\u011bd \u010cesk\u00e9 Republiky","ror":"https://ror.org/053avzc18"},{"id":"https://openalex.org/F4320322748","display_name":"Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b","ror":"https://ror.org/03613d656"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2118714546.pdf","grobid_xml":"https://content.openalex.org/works/W2118714546.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1519266993","https://openalex.org/W1529150233","https://openalex.org/W1964640688","https://openalex.org/W1967682948","https://openalex.org/W1970723316","https://openalex.org/W1972216879","https://openalex.org/W1973002250","https://openalex.org/W1984874903","https://openalex.org/W1988654948","https://openalex.org/W1992170964","https://openalex.org/W1993231572","https://openalex.org/W1999025443","https://openalex.org/W2005862188","https://openalex.org/W2010180565","https://openalex.org/W2027344121","https://openalex.org/W2034451231","https://openalex.org/W2037631993","https://openalex.org/W2057029228","https://openalex.org/W2061533419","https://openalex.org/W2068297182","https://openalex.org/W2068493215","https://openalex.org/W2069663555","https://openalex.org/W2077776336","https://openalex.org/W2080267554","https://openalex.org/W2096525273","https://openalex.org/W2098569746","https://openalex.org/W2103499539","https://openalex.org/W2110515210","https://openalex.org/W2112169196","https://openalex.org/W2116099439","https://openalex.org/W2130479394","https://openalex.org/W2131080603","https://openalex.org/W2131701775","https://openalex.org/W2136758633","https://openalex.org/W2137572220","https://openalex.org/W2138595670","https://openalex.org/W2143315188","https://openalex.org/W2147231162","https://openalex.org/W2154139219","https://openalex.org/W2155480492","https://openalex.org/W2156125289","https://openalex.org/W2156624967","https://openalex.org/W2158714788","https://openalex.org/W2162388472","https://openalex.org/W2163352757","https://openalex.org/W2329156357","https://openalex.org/W2376883917","https://openalex.org/W4250297812"],"related_works":["https://openalex.org/W4252778556","https://openalex.org/W24553703","https://openalex.org/W4211000692","https://openalex.org/W2512851574","https://openalex.org/W4212920271","https://openalex.org/W2612240612","https://openalex.org/W4324018414","https://openalex.org/W4211208250","https://openalex.org/W2803753687","https://openalex.org/W2793278779"],"abstract_inverted_index":{"HotSpot":[0,112,141,173],"Wizard":[1,113,142,174],"is":[2,175],"a":[3],"web":[4,29,136],"server":[5,30,143],"for":[6,12,23,56,106,147,160],"automatic":[7],"identification":[8],"of":[9,14,20,25,63,123,155,163],"'hot":[10,54],"spots'":[11,55],"engineering":[13,34],"substrate":[15],"specificity,":[16],"activity":[17],"or":[18,48],"enantioselectivity":[19],"enzymes":[21],"and":[22,66,81,84,93,98,132,159,168],"annotation":[24],"protein":[26,33,96,148,158],"structures.":[27],"The":[28,53,95,121,140],"implements":[31],"the":[32,45,50,61,72,86,102,107,110,124,129,135,153,161],"protocol,":[35],"which":[36],"targets":[37],"evolutionarily":[38],"variable":[39],"amino":[40],"acid":[41],"positions":[42],"located":[43],"in":[44,134,151,165],"active":[46],"site":[47],"lining":[49],"access":[51],"tunnels.":[52],"mutagenesis":[57,167],"are":[58,101,126],"selected":[59],"through":[60],"integration":[62],"structural,":[64],"functional":[65],"evolutionary":[67],"information":[68],"obtained":[69],"from:":[70],"(i)":[71],"databases":[73],"RCSB":[74],"PDB,":[75],"UniProt,":[76],"PDBSWS,":[77],"Catalytic":[78],"Site":[79],"Atlas":[80],"nr":[82],"NCBI":[83],"(ii)":[85],"tools":[87],"CASTp,":[88],"CAVER,":[89],"BLAST,":[90],"CD-HIT,":[91],"MUSCLE":[92],"Rate4Site.":[94],"structure":[97,131,154],"e-mail":[99],"address":[100],"only":[103],"obligatory":[104],"inputs":[105],"calculation.":[108],"In":[109],"output,":[111],"lists":[114],"annotated":[115],"residues":[116],"ordered":[117],"by":[118],"estimated":[119],"mutability.":[120],"results":[122],"analysis":[125],"mapped":[127],"on":[128],"enzyme":[130],"visualized":[133],"browser":[137],"using":[138],"Jmol.":[139],"should":[144],"be":[145],"useful":[146],"engineers":[149],"interested":[150],"exploring":[152],"their":[156],"favourite":[157],"design":[162],"mutations":[164],"site-directed":[166],"focused":[169],"directed":[170],"evolution":[171],"experiments.":[172],"available":[176],"at":[177],"http://loschmidt.chemi.muni.cz/hotspotwizard/.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":19},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":16}],"updated_date":"2026-09-11T09:22:31.653822","created_date":"2025-10-10T00:00:00"}
