{"id":"https://openalex.org/W1988041911","doi":"https://doi.org/10.1371/journal.pcbi.1003995","title":"Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation","display_name":"Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation","publication_year":2014,"publication_date":"2014-12-11","ids":{"openalex":"https://openalex.org/W1988041911","doi":"https://doi.org/10.1371/journal.pcbi.1003995","mag":"1988041911","pmid":"https://pubmed.ncbi.nlm.nih.gov/25500811"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003995","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003995","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003995&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003995&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084266902","display_name":"Michael Graf","orcid":"https://orcid.org/0000-0002-4879-3834"},"institutions":[{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Michael M. H. Graf","raw_affiliation_strings":["Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria","institution_ids":["https://openalex.org/I92869138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100835538","display_name":"Lin Zhixiong","orcid":null},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lin Zhixiong","raw_affiliation_strings":["Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I5124864","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003060699","display_name":"Urban Bren","orcid":"https://orcid.org/0000-0002-8806-3019"},"institutions":[{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]},{"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":["AT","SI"],"is_corresponding":false,"raw_author_name":"Urban Bren","raw_affiliation_strings":["Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia","Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria","Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":[]},{"raw_affiliation_string":"Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria","institution_ids":["https://openalex.org/I92869138"]},{"raw_affiliation_string":"Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081657582","display_name":"Dietmar Haltrich","orcid":"https://orcid.org/0000-0002-8722-8176"},"institutions":[{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Dietmar Haltrich","raw_affiliation_strings":["Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria","institution_ids":["https://openalex.org/I92869138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063856246","display_name":"Wilfred F. van Gunsteren","orcid":"https://orcid.org/0000-0002-9583-7019"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Wilfred F. van Gunsteren","raw_affiliation_strings":["Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I5124864","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050713464","display_name":"Chris Oostenbrink","orcid":"https://orcid.org/0000-0002-4232-2556"},"institutions":[{"id":"https://openalex.org/I92869138","display_name":"BOKU University","ror":"https://ror.org/057ff4y42","country_code":"AT","type":"education","lineage":["https://openalex.org/I92869138"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Chris Oostenbrink","raw_affiliation_strings":["Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria","institution_ids":["https://openalex.org/I92869138"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5050713464"],"corresponding_institution_ids":["https://openalex.org/I92869138"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":1766,"currency":"EUR","value_usd":1904},"fwci":0.5691,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.66137523,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"10","issue":"12","first_page":"e1003995","last_page":"e1003995"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9993000030517578,"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":0.9993000030517578,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11136","display_name":"Enzyme-mediated dye degradation","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pyranose","display_name":"Pyranose","score":0.8865437507629395},{"id":"https://openalex.org/keywords/monosaccharide","display_name":"Monosaccharide","score":0.6872297525405884},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6765406131744385},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.5120328068733215},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.49127382040023804},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"Free energy perturbation","score":0.4590439200401306},{"id":"https://openalex.org/keywords/dehydrogenase","display_name":"Dehydrogenase","score":0.4558599591255188},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4063366651535034},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.31444287300109863},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.22757241129875183},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.21779632568359375},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.17026549577713013}],"concepts":[{"id":"https://openalex.org/C34490408","wikidata":"https://www.wikidata.org/wiki/Q424248","display_name":"Pyranose","level":2,"score":0.8865437507629395},{"id":"https://openalex.org/C118859902","wikidata":"https://www.wikidata.org/wiki/Q133516","display_name":"Monosaccharide","level":2,"score":0.6872297525405884},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6765406131744385},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.5120328068733215},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.49127382040023804},{"id":"https://openalex.org/C162641036","wikidata":"https://www.wikidata.org/wiki/Q5500215","display_name":"Free energy perturbation","level":3,"score":0.4590439200401306},{"id":"https://openalex.org/C2776317432","wikidata":"https://www.wikidata.org/wiki/Q412547","display_name":"Dehydrogenase","level":3,"score":0.4558599591255188},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4063366651535034},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.31444287300109863},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.22757241129875183},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.21779632568359375},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.17026549577713013}],"mesh":[{"descriptor_ui":"D000364","descriptor_name":"Agaricus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D000364","descriptor_name":"Agaricus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D000364","descriptor_name":"Agaricus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D000364","descriptor_name":"Agaricus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009005","descriptor_name":"Monosaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1003995","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003995","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003995&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25500811","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25500811","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:c7682c21f6d841789ed682e3520310c4","is_oa":true,"landing_page_url":"https://doaj.org/article/c7682c21f6d841789ed682e3520310c4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 12, p e1003995 (2014)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1268047","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Pyranose_Dehydrogenase_Ligand_Promiscuity_A_Generalized_Approach_to_Simulate_Monosaccharide_Solvation_Binding_and_Product_Formation_/1268047","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4263366","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4263366","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003995","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003995","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003995&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.5,"display_name":"Affordable and clean energy"},{"id":"https://metadata.un.org/sdg/6","score":0.41999998688697815,"display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G176856287","display_name":"Biomolecular Simulation of Biomolecular Systems II","funder_award_id":"137827","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G3077098309","display_name":null,"funder_award_id":"LS08-QM03","funder_id":"https://openalex.org/F4320321003","funder_display_name":"Vienna Science and Technology Fund"},{"id":"https://openalex.org/G3981829596","display_name":"Biomolecular Technology of Proteins - BioToP","funder_award_id":"W1224","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G4311008617","display_name":null,"funder_award_id":"228076","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G5599649393","display_name":null,"funder_award_id":"200020","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5707902099","display_name":null,"funder_award_id":"J1-5448","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G6070106675","display_name":null,"funder_award_id":"P1-0002","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G628552264","display_name":null,"funder_award_id":"200020","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G651422904","display_name":null,"funder_award_id":"200020-137827","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G6790186255","display_name":null,"funder_award_id":"228076","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321003","display_name":"Vienna Science and Technology Fund","ror":"https://ror.org/01f9mc681"},{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"},{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1988041911.pdf","grobid_xml":"https://content.openalex.org/works/W1988041911.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W608234513","https://openalex.org/W617643828","https://openalex.org/W626094067","https://openalex.org/W1491824558","https://openalex.org/W1493551869","https://openalex.org/W1501687440","https://openalex.org/W1625910593","https://openalex.org/W1964021249","https://openalex.org/W1965436581","https://openalex.org/W1965877980","https://openalex.org/W1968583410","https://openalex.org/W1972697502","https://openalex.org/W1982821267","https://openalex.org/W1986055915","https://openalex.org/W1989753444","https://openalex.org/W1992625839","https://openalex.org/W1993177346","https://openalex.org/W1996226840","https://openalex.org/W2003108724","https://openalex.org/W2003791843","https://openalex.org/W2011650148","https://openalex.org/W2013058730","https://openalex.org/W2019502364","https://openalex.org/W2022832357","https://openalex.org/W2022976866","https://openalex.org/W2024772565","https://openalex.org/W2027154929","https://openalex.org/W2031418794","https://openalex.org/W2035266068","https://openalex.org/W2044172420","https://openalex.org/W2058637683","https://openalex.org/W2060189458","https://openalex.org/W2060849434","https://openalex.org/W2068481735","https://openalex.org/W2071100966","https://openalex.org/W2078188549","https://openalex.org/W2079827331","https://openalex.org/W2087326178","https://openalex.org/W2088547439","https://openalex.org/W2103731920","https://openalex.org/W2103945336","https://openalex.org/W2106140689","https://openalex.org/W2106531843","https://openalex.org/W2110198171","https://openalex.org/W2121723608","https://openalex.org/W2124159639","https://openalex.org/W2127522551","https://openalex.org/W2128312954","https://openalex.org/W2129213941","https://openalex.org/W2133155377","https://openalex.org/W2134441341","https://openalex.org/W2135900956","https://openalex.org/W2146020438","https://openalex.org/W2156238280","https://openalex.org/W2157553215","https://openalex.org/W2164497185","https://openalex.org/W2343863355","https://openalex.org/W2397040980","https://openalex.org/W2419670049"],"related_works":["https://openalex.org/W2296214532","https://openalex.org/W4229747608","https://openalex.org/W4252174712","https://openalex.org/W2282374326","https://openalex.org/W2237020303","https://openalex.org/W2050023963","https://openalex.org/W4376877131","https://openalex.org/W4211111046","https://openalex.org/W2038702052","https://openalex.org/W2089807142"],"abstract_inverted_index":{"The":[0,86,130,149,272],"flavoenzyme":[1],"pyranose":[2],"dehydrogenase":[3],"(PDH)":[4],"from":[5,127,146],"the":[6,42,60,66,84,110,115,157,161,166,180,183,187,220,253],"litter":[7],"decomposing":[8],"fungus":[9],"Agaricus":[10],"meleagris":[11],"oxidizes":[12],"many":[13],"different":[14,123],"carbohydrates":[15],"occurring":[16],"during":[17],"lignin":[18],"degradation.":[19],"This":[20,250],"promiscuous":[21],"substrate":[22,260],"specificity":[23],"makes":[24],"PDH":[25,120],"a":[26,47,106,228,276],"promising":[27],"catalyst":[28],"for":[29,154,169,201,209,219,238,267],"bioelectrochemical":[30],"applications.":[31],"A":[32],"generalized":[33],"approach":[34,278],"to":[35,59,102,119,142,282],"simulate":[36],"all":[37,72,96],"32":[38,73,116],"possible":[39,196],"aldohexopyranoses":[40,74],"in":[41,75,83,98,121,159,165,262,270],"course":[43],"of":[44,71,95,114,156,179,186,222,285],"one":[45,155],"or":[46,173,199,207],"few":[48],"molecular":[49],"dynamics":[50],"(MD)":[51],"simulations":[52],"is":[53,195],"reported.":[54],"Free":[55],"energy":[56,88],"calculations":[57],"according":[58],"one-step":[61],"perturbation":[62],"(OSP)":[63],"method":[64],"revealed":[65,192],"solvation":[67],"free":[68,87,133,257],"energies":[69,134,258],"(\u0394Gsolv)":[70],"water,":[76],"which":[77,160],"have":[78,241],"not":[79,242],"yet":[80,243],"been":[81,244],"reported":[82],"literature.":[85],"difference":[89],"between":[90,177,255],"\u03b2-":[91],"and":[92,182,204,227,259],"\u03b1-anomers":[93],"(\u0394G\u03b2-\u03b1)":[94],"d-stereoisomers":[97],"water":[99],"were":[100,125,136,236],"compared":[101,141],"experimental":[103,143],"values":[104],"with":[105],"good":[107,153],"agreement.":[108],"Moreover,":[109],"free-energy":[111],"differences":[112],"(\u0394G)":[113],"stereoisomers":[117],"bound":[118],"two":[122],"poses":[124],"calculated":[126,137],"MD":[128],"simulations.":[129],"relative":[131],"binding":[132,256],"(\u0394\u0394Gbind)":[135],"and,":[138],"where":[139],"available,":[140],"values,":[144],"approximated":[145],"Km":[147],"values.":[148],"agreement":[150],"was":[151],"very":[152],"poses,":[158],"sugars":[162,239],"are":[163],"positioned":[164],"active":[167],"site":[168],"oxidation":[170,194,214,234],"at":[171,197,205],"C1":[172],"C2.":[174],"Distance":[175],"analysis":[176],"hydrogens":[178],"monosaccharide":[181],"reactive":[184],"N5-atom":[185],"flavin":[188],"adenine":[189],"dinucleotide":[190],"(FAD)":[191],"that":[193,240,275],"HC1":[198],"HC2":[200],"pose":[202,210],"A,":[203],"HC3":[206],"HC4":[208],"B.":[211],"Experimentally":[212],"detected":[213],"products":[215,235],"could":[216,279],"be":[217,280],"rationalized":[218],"majority":[221],"monosaccharides":[223],"by":[224],"combining":[225],"\u0394\u0394Gbind":[226],"reweighted":[229],"distance":[230],"analysis.":[231],"Furthermore,":[232],"several":[233],"predicted":[237],"tested":[245],"experimentally,":[246],"directing":[247],"further":[248],"analyses.":[249],"study":[251,283],"rationalizes":[252],"relationship":[254],"promiscuity":[261,284],"PDH,":[263],"providing":[264],"novel":[265],"insights":[266],"its":[268],"applicability":[269],"bioelectrochemistry.":[271],"results":[273],"suggest":[274],"similar":[277],"applied":[281],"other":[286],"enzymes.":[287]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
