{"id":"https://openalex.org/W2005820168","doi":"https://doi.org/10.1007/s10822-010-9369-x","title":"Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin\u2014an insight from molecular dynamics simulations with classical and ab initio force fields","display_name":"Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin\u2014an insight from molecular dynamics simulations with classical and ab initio force fields","publication_year":2010,"publication_date":"2010-06-04","ids":{"openalex":"https://openalex.org/W2005820168","doi":"https://doi.org/10.1007/s10822-010-9369-x","mag":"2005820168","pmid":"https://pubmed.ncbi.nlm.nih.gov/20526651"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-010-9369-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-010-9369-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9369-x.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9369-x.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088189844","display_name":"Jaros\u0142aw J. Panek","orcid":"https://orcid.org/0000-0002-2952-9739"},"institutions":[{"id":"https://openalex.org/I219388962","display_name":"University of Wroc\u0142aw","ror":"https://ror.org/00yae6e25","country_code":"PL","type":"education","lineage":["https://openalex.org/I219388962"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Jaros\u0142aw J. Panek","raw_affiliation_strings":["Faculty of Chemistry, University of Wroc\u0142aw, ul. F. Joliot-Curie 14, 50-383 Wroc\u0142aw, Poland. jarek@elrond.chem.uni.wroc.pl","Faculty of Chemistry, University of Wroc\u0142aw, ul. F. Joliot-Curie 14, 50-383, Wroc\u0142aw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Wroc\u0142aw, ul. F. Joliot-Curie 14, 50-383 Wroc\u0142aw, Poland. jarek@elrond.chem.uni.wroc.pl","institution_ids":["https://openalex.org/I219388962"]},{"raw_affiliation_string":"Faculty of Chemistry, University of Wroc\u0142aw, ul. F. Joliot-Curie 14, 50-383, Wroc\u0142aw, Poland","institution_ids":["https://openalex.org/I219388962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057806953","display_name":"Thomas R. Ward","orcid":"https://orcid.org/0000-0001-8602-5468"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Thomas R. Ward","raw_affiliation_strings":["Department of Chemistry, University of Basel, Spitalstrasse 51, 4056, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Basel, Spitalstrasse 51, 4056, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059871664","display_name":"Aneta Jezierska","orcid":"https://orcid.org/0000-0001-6601-9124"},"institutions":[{"id":"https://openalex.org/I219388962","display_name":"University of Wroc\u0142aw","ror":"https://ror.org/00yae6e25","country_code":"PL","type":"education","lineage":["https://openalex.org/I219388962"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["PL","SI"],"is_corresponding":false,"raw_author_name":"Aneta Jezierska-Mazzarello","raw_affiliation_strings":["Faculty of Chemistry, University of Wroc\u0142aw, ul. F. Joliot-Curie 14, 50-383, Wroc\u0142aw, Poland","National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Wroc\u0142aw, ul. F. Joliot-Curie 14, 50-383, Wroc\u0142aw, Poland","institution_ids":["https://openalex.org/I219388962"]},{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113656739","display_name":"Marjana Novi\u010d","orcid":null},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Marjana Novi\u010d","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088189844"],"corresponding_institution_ids":["https://openalex.org/I219388962"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":0.1673,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.53640023,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"24","issue":"9","first_page":"719","last_page":"732"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11611","display_name":"Cyclopropane Reaction Mechanisms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11611","display_name":"Cyclopropane Reaction Mechanisms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11626","display_name":"Metalloenzymes and iron-sulfur proteins","score":0.9947999715805054,"subfield":{"id":"https://openalex.org/subfields/2105","display_name":"Renewable Energy, Sustainability and the Environment"},"field":{"id":"https://openalex.org/fields/21","display_name":"Energy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biotinylation","display_name":"Biotinylation","score":0.8380590677261353},{"id":"https://openalex.org/keywords/streptavidin","display_name":"Streptavidin","score":0.7294817566871643},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.699235737323761},{"id":"https://openalex.org/keywords/moiety","display_name":"Moiety","score":0.6573854684829712},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.6116604208946228},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5450563430786133},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5295425653457642},{"id":"https://openalex.org/keywords/cofactor","display_name":"Cofactor","score":0.48643946647644043},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.4698570966720581},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4571102261543274},{"id":"https://openalex.org/keywords/molecular-recognition","display_name":"Molecular recognition","score":0.4361095428466797},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.32401877641677856},{"id":"https://openalex.org/keywords/biotin","display_name":"Biotin","score":0.3018031716346741},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2589260935783386},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.18618318438529968},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.11914536356925964},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.11642178893089294},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09873577952384949},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.08791515231132507}],"concepts":[{"id":"https://openalex.org/C204628709","wikidata":"https://www.wikidata.org/wiki/Q864854","display_name":"Biotinylation","level":2,"score":0.8380590677261353},{"id":"https://openalex.org/C2776190903","wikidata":"https://www.wikidata.org/wiki/Q421817","display_name":"Streptavidin","level":3,"score":0.7294817566871643},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.699235737323761},{"id":"https://openalex.org/C2776568683","wikidata":"https://www.wikidata.org/wiki/Q23005640","display_name":"Moiety","level":2,"score":0.6573854684829712},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.6116604208946228},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5450563430786133},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5295425653457642},{"id":"https://openalex.org/C197957613","wikidata":"https://www.wikidata.org/wiki/Q407280","display_name":"Cofactor","level":3,"score":0.48643946647644043},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.4698570966720581},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4571102261543274},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.4361095428466797},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.32401877641677856},{"id":"https://openalex.org/C2778204606","wikidata":"https://www.wikidata.org/wiki/Q181354","display_name":"Biotin","level":2,"score":0.3018031716346741},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2589260935783386},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.18618318438529968},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.11914536356925964},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.11642178893089294},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09873577952384949},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.08791515231132507}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001710","descriptor_name":"Biotin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007659","descriptor_name":"Ketones","qualifier_ui":"Q000138","qualifier_name":"chemical synthesis","is_major_topic":false},{"descriptor_ui":"D007659","descriptor_name":"Ketones","qualifier_ui":"Q000138","qualifier_name":"chemical synthesis","is_major_topic":false},{"descriptor_ui":"D007659","descriptor_name":"Ketones","qualifier_ui":"Q000138","qualifier_name":"chemical synthesis","is_major_topic":false},{"descriptor_ui":"D007659","descriptor_name":"Ketones","qualifier_ui":"Q000138","qualifier_name":"chemical synthesis","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016297","descriptor_name":"Mutagenesis, Site-Directed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019809","descriptor_name":"Streptavidin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-010-9369-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-010-9369-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9369-x.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:20526651","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20526651","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2918797","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2918797","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-010-9369-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-010-9369-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9369-x.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G3176773552","display_name":null,"funder_award_id":"P1-017","funder_id":"https://openalex.org/F4320327264","funder_display_name":"Ministrstvo za visoko \u0161olstvo, znanost in tehnologijo"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320327264","display_name":"Ministrstvo za visoko \u0161olstvo, znanost in tehnologijo","ror":"https://ror.org/0452h9305"},{"id":"https://openalex.org/F4320335596","display_name":"Wroclawskie Centrum Sieciowo-Superkomputerowe, Politechnika Wroclawska","ror":null},{"id":"https://openalex.org/F4320337160","display_name":"Academic Computer Centre Cyfronet, AGH University of Science and Technology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2005820168.pdf","grobid_xml":"https://content.openalex.org/works/W2005820168.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1510114475","https://openalex.org/W1966808493","https://openalex.org/W1976499671","https://openalex.org/W1982952953","https://openalex.org/W1984622104","https://openalex.org/W1985729209","https://openalex.org/W1988284526","https://openalex.org/W1988715261","https://openalex.org/W1989060947","https://openalex.org/W1998524463","https://openalex.org/W2001368737","https://openalex.org/W2001936871","https://openalex.org/W2005521680","https://openalex.org/W2014166972","https://openalex.org/W2014960272","https://openalex.org/W2015723183","https://openalex.org/W2017001642","https://openalex.org/W2017196167","https://openalex.org/W2023271753","https://openalex.org/W2028257896","https://openalex.org/W2028908168","https://openalex.org/W2029667189","https://openalex.org/W2030976617","https://openalex.org/W2035687084","https://openalex.org/W2038096044","https://openalex.org/W2038758364","https://openalex.org/W2039962975","https://openalex.org/W2041638382","https://openalex.org/W2048791198","https://openalex.org/W2049118022","https://openalex.org/W2051362165","https://openalex.org/W2059124617","https://openalex.org/W2060470134","https://openalex.org/W2067174909","https://openalex.org/W2070390193","https://openalex.org/W2074606375","https://openalex.org/W2079651052","https://openalex.org/W2083758034","https://openalex.org/W2083938871","https://openalex.org/W2085560162","https://openalex.org/W2086957099","https://openalex.org/W2092945086","https://openalex.org/W2100059026","https://openalex.org/W2102537419","https://openalex.org/W2104554134","https://openalex.org/W2106140689","https://openalex.org/W2110466770","https://openalex.org/W2111197146","https://openalex.org/W2118363414","https://openalex.org/W2120612993","https://openalex.org/W2121224201","https://openalex.org/W2127378318","https://openalex.org/W2127664963","https://openalex.org/W2128276019","https://openalex.org/W2143981217","https://openalex.org/W2144288821","https://openalex.org/W2150394181","https://openalex.org/W2162415535","https://openalex.org/W2171999733","https://openalex.org/W2230728100","https://openalex.org/W2311078281","https://openalex.org/W2321038980","https://openalex.org/W2552822738","https://openalex.org/W2951807258","https://openalex.org/W4211027922","https://openalex.org/W6600100803"],"related_works":["https://openalex.org/W2067031238","https://openalex.org/W4293102437","https://openalex.org/W2026593038","https://openalex.org/W2070869769","https://openalex.org/W4205773778","https://openalex.org/W2072176055","https://openalex.org/W2923238538","https://openalex.org/W1985110858","https://openalex.org/W2155124271","https://openalex.org/W2054902093"],"abstract_inverted_index":{"In":[0],"the":[1,32,56,77,91,107,126,133,142,153,164,178,187,202,220,232,243],"field":[2,104],"of":[3,18,34,43,58,67,98,129,170,180,189,201,231],"enzymatic":[4],"catalysis,":[5],"creating":[6],"activity":[7],"from":[8],"a":[9,14,19,24,44,68,197,205],"non":[10],"catalytic":[11,208],"scaffold":[12,26],"is":[13,174],"daunting":[15],"task.":[16],"Introduction":[17],"catalytically":[20],"active":[21],"moiety":[22],"within":[23,48],"protein":[25,143,240],"offers":[27],"an":[28,63,190],"attractive":[29],"means":[30],"for":[31,55,228],"creation":[33],"artificial":[35,53],"metalloenzymes.":[36],"With":[37],"this":[38,161],"goal":[39],"in":[40,163],"mind,":[41],"introduction":[42],"biotinylated":[45,78,192],"d(6)-piano-stool":[46],"complex":[47],"streptavidin":[49],"(SAV)":[50],"affords":[51],"enantioselective":[52],"transfer-hydrogenases":[54],"reduction":[57],"prochiral":[59],"ketones.":[60],"Based":[61],"on":[62,83,90],"X-ray":[64],"crystal":[65],"structure":[66],"highly":[69],"selective":[70],"hybrid":[71],"catalyst,":[72],"displaying":[73],"significant":[74],"disorder":[75],"around":[76],"catalyst":[79],"[eta(6)-(p-cymene)Ru(Biot-p-L)Cl],":[80],"we":[81],"report":[82],"molecular":[84],"dynamics":[85],"simulations":[86,100],"to":[87,141,148,159,196],"shed":[88],"light":[89],"protein-cofactor":[92],"interactions":[93],"and":[94,109,152,204,248],"contacts.":[95],"The":[96,118,145,168,234],"results":[97],"these":[99],"with":[101,213],"classical":[102],"force":[103],"indicate":[105],"that":[106,219],"SAV-biotin":[108],"SAV-catalyst":[110],"complexes":[111],"are":[112,224],"more":[113],"stable":[114],"than":[115],"ligand-free":[116],"SAV.":[117],"point":[119],"mutations":[120],"introduced":[121],"did":[122,136],"not":[123,137,225],"affect":[124],"significantly":[125],"overall":[127],"behavior":[128],"SAV":[130],"and,":[131],"unexpectedly,":[132],"P64G":[134,156],"substitution":[135],"provide":[138],"additional":[139],"flexibility":[140],"scaffold.":[144],"metal-cofactor":[146],"proved":[147,158],"be":[149],"conformationally":[150],"flexible,":[151],"S112K":[154],"or":[155],"mutants":[157],"enhance":[160],"effect":[162],"most":[165],"pronounced":[166],"way.":[167],"network":[169],"intermolecular":[171],"hydrogen":[172,221,244],"bonds":[173,222,245],"efficient":[175],"at":[176,185],"stabilizing":[177],"position":[179],"biotin,":[181],"but":[182],"much":[183],"less":[184],"fixing":[186],"conformation":[188],"extended":[191],"ligand.":[193],"This":[194],"leads":[195],"relative":[198],"conformational":[199],"freedom":[200],"metal-cofactor,":[203],"poorly":[206],"localized":[207],"metal":[209],"moiety.":[210],"MD":[211],"calculations":[212],"ab":[214],"initio":[215],"potential":[216],"function":[217],"suggest":[218],"alone":[223],"sufficient":[226],"factors":[227],"full":[229],"stabilization":[230],"biotin.":[233],"hydrophobic":[235],"biotin-binding":[236],"pocket":[237],"(and":[238],"generally":[239],"scaffold)":[241],"maintains":[242],"between":[246],"biotin":[247],"protein.":[249]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
