{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T08:05:25Z","timestamp":1772784325380,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T00:00:00Z","timestamp":1527033600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Programme of Sustainability II","award":["LQ1602"],"award-info":[{"award-number":["LQ1602"]}]},{"name":"National Programme of Sustainability II","award":["LQ1605"],"award-info":[{"award-number":["LQ1605"]}]},{"name":"National Programme of Sustainability II","award":["LO1214"],"award-info":[{"award-number":["LO1214"]}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["LM2015051"],"award-info":[{"award-number":["LM2015051"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["LM2015047"],"award-info":[{"award-number":["LM2015047"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["LM2015055"],"award-info":[{"award-number":["LM2015055"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Grant Agency of the Czech Republic","doi-asserted-by":"publisher","award":["16-06096S"],"award-info":[{"award-number":["16-06096S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000807","name":"European Union","doi-asserted-by":"publisher","award":["720776"],"award-info":[{"award-number":["720776"]}],"id":[{"id":"10.13039\/501100000807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000807","name":"European Union","doi-asserted-by":"publisher","award":["722610"],"award-info":[{"award-number":["722610"]}],"id":[{"id":"10.13039\/501100000807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004585","name":"Brno University of Technology","doi-asserted-by":"publisher","award":["FIT-S-17-3994"],"award-info":[{"award-number":["FIT-S-17-3994"]}],"id":[{"id":"10.13039\/501100004585","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,2]]},"DOI":"10.1093\/nar\/gky417","type":"journal-article","created":{"date-parts":[[2018,5,7]],"date-time":"2018-05-07T19:14:31Z","timestamp":1525720471000},"page":"W356-W362","source":"Crossref","is-referenced-by-count":293,"title":["HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information"],"prefix":"10.1093","volume":"46","author":[{"given":"Lenka","family":"Sumbalova","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, 62500\u00a0Brno, Czech Republic"},{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Bozetechova 2, 61266 Brno, Czech Republic"}]},{"given":"Jan","family":"Stourac","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, 62500\u00a0Brno, Czech Republic"},{"name":"International Centre for Clinical Research, St. Anne\u2019s University Hospital Brno, 65691\u00a0Brno, Czech Republic"}]},{"given":"Tomas","family":"Martinek","sequence":"additional","affiliation":[{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Bozetechova 2, 61266 Brno, Czech Republic"}]},{"given":"David","family":"Bednar","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, 62500\u00a0Brno, Czech Republic"},{"name":"International Centre for Clinical Research, St. Anne\u2019s University Hospital Brno, 65691\u00a0Brno, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7848-8216","authenticated-orcid":false,"given":"Jiri","family":"Damborsky","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, 62500\u00a0Brno, Czech Republic"},{"name":"International Centre for Clinical Research, St. Anne\u2019s University Hospital Brno, 65691\u00a0Brno, Czech Republic"}]}],"member":"286","published-online":{"date-parts":[[2018,5,23]]},"reference":[{"key":"key\n\t\t\t\t20180630061752_B1","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1016\/j.addr.2007.08.044","article-title":"Protein nanoparticles as drug carriers in clinical medicine","volume":"60","author":"Hawkins","year":"2008","journal-title":"Adv. Drug Deliv. Rev."},{"key":"key\n\t\t\t\t20180630061752_B2","first-page":"582","article-title":"Industrial applications","volume-title":"Industrial Enzymology: The Application of Enzymes in Industry","author":"Godfrey","year":"1982"},{"key":"key\n\t\t\t\t20180630061752_B3","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1021\/cb700249v","article-title":"Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems","volume":"3","author":"Bromley","year":"2008","journal-title":"ACS Chem. Biol."},{"key":"key\n\t\t\t\t20180630061752_B4","doi-asserted-by":"crossref","first-page":"3499","DOI":"10.1039\/b917574c","article-title":"Applications of peptide and protein-based materials in bionanotechnology","volume":"39","author":"De\u00a0La\u00a0Rica","year":"2010","journal-title":"Chem. Soc. Rev."},{"key":"key\n\t\t\t\t20180630061752_B5","doi-asserted-by":"crossref","first-page":"9760","DOI":"10.1039\/C5CC01594D","article-title":"Directed evolution 2.0: improving and deciphering enzyme properties","volume":"51","author":"Cheng","year":"2015","journal-title":"Chem. Commun."},{"key":"key\n\t\t\t\t20180630061752_B6","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1038\/nrm2805","article-title":"Exploring protein fitness landscapes by directed evolution","volume":"10","author":"Romero","year":"2009","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"key\n\t\t\t\t20180630061752_B7","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.copbio.2010.08.011","article-title":"Beyond directed evolution\u2014semi-rational protein engineering and design","volume":"21","author":"Lutz","year":"2010","journal-title":"Curr. Opin. Biotechnol."},{"key":"key\n\t\t\t\t20180630061752_B8","first-page":"1","article-title":"Identification of key residues modulating the stereoselectivity of nitrile hydratase towards rac\u2010Mandelonitrile by Semi\u2010rational engineering","volume":"115","author":"Cheng","year":"2017","journal-title":"Biotechnol. Bioeng."},{"key":"key\n\t\t\t\t20180630061752_B9","doi-asserted-by":"crossref","first-page":"W479","DOI":"10.1093\/nar\/gkw416","article-title":"HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering","volume":"44","author":"Bendl","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B10","first-page":"220","article-title":"Oxy-haemoglobin protein engineering: an automated design for hotspots stability, site-specific mutations and smart libraries by using HotSpot Wizard 2.0 software","volume":"8","author":"Talukdar","year":"2017","journal-title":"Int. J. Adv. Res. Comput. Sci."},{"key":"key\n\t\t\t\t20180630061752_B11","doi-asserted-by":"crossref","first-page":"15287","DOI":"10.1038\/s41598-017-12659-y","article-title":"Thermostability improvement of a Talaromyces leycettanus xylanase by rational protein engineering","volume":"7","author":"Wang","year":"2017","journal-title":"Sci. Rep."},{"key":"key\n\t\t\t\t20180630061752_B12","first-page":"1","article-title":"Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis","volume":"35","author":"Vatansever","year":"2016","journal-title":"J. Biomol. Struct. Dyn."},{"key":"key\n\t\t\t\t20180630061752_B13","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B14","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"UniProt Consortium","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B15","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1126\/science.1065659","article-title":"Protein structure prediction and structural genomics","volume":"294","author":"Baker","year":"2001","journal-title":"Science"},{"key":"key\n\t\t\t\t20180630061752_B16","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1016\/j.drudis.2009.04.006","article-title":"Homology modeling in drug discovery: current trends and applications","volume":"14","author":"Cavasotto","year":"2009","journal-title":"Drug Discov. Today"},{"key":"key\n\t\t\t\t20180630061752_B17","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1016\/j.str.2013.08.007","article-title":"Protein modeling: what happened to the \u2018protein structure gap\u2019","volume":"21","author":"Schwede","year":"2013","journal-title":"Structure"},{"key":"key\n\t\t\t\t20180630061752_B18","doi-asserted-by":"crossref","first-page":"bat031","DOI":"10.1093\/database\/bat031","article-title":"The Protein Model Portal\u2014a comprehensive resource for protein structure and model information","volume":"2013","author":"Haas","year":"2013","journal-title":"Database"},{"key":"key\n\t\t\t\t20180630061752_B19","article-title":"CSMP | Home","author":"Csmp.ucsf.edu","year":"2017"},{"key":"key\n\t\t\t\t20180630061752_B20","article-title":"The Joint Center for Structural Genomics (JCSG) Homepage","author":"Jcsg.org","year":"2017"},{"key":"key\n\t\t\t\t20180630061752_B21","author":"Mcsg.anl.gov","year":"2017"},{"key":"key\n\t\t\t\t20180630061752_B22","article-title":"NESG - NorthEast Structural Genomics consortium","author":"Nesg.org","year":"2017"},{"key":"key\n\t\t\t\t20180630061752_B23","article-title":"NYSGRC","author":"Venkatagiriyappa","year":"2017"},{"key":"key\n\t\t\t\t20180630061752_B24","article-title":"Joint Center for Molecular Modeling (JCMM)","author":"Jcmm.burnham.org","year":"2017"},{"key":"key\n\t\t\t\t20180630061752_B25","doi-asserted-by":"crossref","first-page":"D336","DOI":"10.1093\/nar\/gkt1144","article-title":"ModBase, a database of annotated comparative protein structure models and associated resources","volume":"42","author":"Pieper","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B26","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkn750","article-title":"The SWISS-MODEL repository and associated resources","volume":"37","author":"Kiefer","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B27","doi-asserted-by":"crossref","first-page":"W252","DOI":"10.1093\/nar\/gku340","article-title":"SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information","volume":"42","author":"Biasini","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B28","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1016\/j.str.2013.08.005","article-title":"High-resolution comparative modeling with RosettaCM","volume":"21","author":"Song","year":"2013","journal-title":"Structure"},{"key":"key\n\t\t\t\t20180630061752_B29","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"Kim","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B30","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20180630061752_B31","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/bioinformatics\/btq664","article-title":"Improved predictions by Pcons. net using multiple templates","volume":"27","author":"Larsson","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630061752_B32","first-page":"151","article-title":"Protein structure modeling with MODELLER","volume":"1137","author":"Webb","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20180630061752_B33","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: protein structure and function prediction","volume":"12","author":"Yang","year":"2015","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180630061752_B34","doi-asserted-by":"crossref","first-page":"W169","DOI":"10.1093\/nar\/gkv236","article-title":"IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences","volume":"43","author":"McGuffin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B35","doi-asserted-by":"crossref","first-page":"e1001244","DOI":"10.1371\/journal.pbio.1001244","article-title":"Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies","volume":"10","author":"Russel","year":"2012","journal-title":"PLoS Biol."},{"key":"key\n\t\t\t\t20180630061752_B36","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/prot.22499","article-title":"Fast and accurate automatic structure prediction with HHpred","volume":"77","author":"Hildebrand","year":"2009","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630061752_B37","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1038\/nprot.2012.085","article-title":"Template-based protein structure modeling using the RaptorX web server","volume":"7","author":"K\u00e4llberg","year":"2012","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20180630061752_B38","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/btr350","article-title":"Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates","volume":"27","author":"Yang","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630061752_B39","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1002\/prot.24448","article-title":"CASP10 results compared to those of previous CASP experiments","volume":"82","author":"Kryshtafovych","year":"2014","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630061752_B40","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. Appl. Crystallogr."},{"key":"key\n\t\t\t\t20180630061752_B41","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: all-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"key\n\t\t\t\t20180630061752_B42","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/381272a0","article-title":"Errors in protein structures","volume":"381","author":"Hooft","year":"1996","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180630061752_B43","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1002\/prot.22921","article-title":"Role of conformational sampling in computing mutation\u2010induced changes in protein structure and stability","volume":"79","author":"Kellogg","year":"2011","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630061752_B44","doi-asserted-by":"crossref","first-page":"W382","DOI":"10.1093\/nar\/gki387","article-title":"The FoldX web server: an online force field","volume":"33","author":"Schymkowitz","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061752_B45","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1002\/prot.22921","article-title":"Role of conformational sampling in computing mutation\u2010induced changes in protein structure and stability","volume":"79","author":"Kellogg","year":"2011","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20180630061752_B46","doi-asserted-by":"crossref","first-page":"e1004556","DOI":"10.1371\/journal.pcbi.1004556","article-title":"FireProt: energy-and evolution-based computational design of thermostable multiple-point mutants","volume":"11","author":"Bednar","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20180630061752_B47","doi-asserted-by":"crossref","first-page":"52622","DOI":"10.1074\/jbc.M306762200","article-title":"Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel","volume":"278","author":"Chaloupkov\u00e1","year":"2003","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20180630061752_B48","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.1128\/AEM.69.4.2349-2355.2003","article-title":"Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB","volume":"69","author":"Nagata","year":"2003","journal-title":"Appl. Environ. Microbiol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/W1\/W356\/25110355\/gky417.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,17]],"date-time":"2019-10-17T17:34:52Z","timestamp":1571333692000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/46\/W1\/W356\/5001543"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,23]]},"references-count":48,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2018,5,23]]},"published-print":{"date-parts":[[2018,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky417","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,2]]},"published":{"date-parts":[[2018,5,23]]}}}