{"id":"https://openalex.org/W3203975617","doi":"https://doi.org/10.1371/journal.pcbi.1009448","title":"dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design","display_name":"dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design","publication_year":2021,"publication_date":"2021-09-27","ids":{"openalex":"https://openalex.org/W3203975617","doi":"https://doi.org/10.1371/journal.pcbi.1009448","mag":"3203975617","pmid":"https://pubmed.ncbi.nlm.nih.gov/34570771"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009448","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009448","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1009448","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101997378","display_name":"Lin Wang","orcid":"https://orcid.org/0000-0002-9455-5570"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Wang","raw_affiliation_strings":["Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016669077","display_name":"Vikas Upadhyay","orcid":"https://orcid.org/0000-0003-2266-5073"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vikas Upadhyay","raw_affiliation_strings":["Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America"],"raw_orcid":"https://orcid.org/0000-0003-2266-5073","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083581014","display_name":"Costas D. Maranas","orcid":"https://orcid.org/0000-0002-1508-1398"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Costas D. Maranas","raw_affiliation_strings":["Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America"],"raw_orcid":"https://orcid.org/0000-0002-1508-1398","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States America","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5083581014"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1882,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.78424027,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"9","first_page":"e1009448","last_page":"e1009448"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9987000226974487,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gibbs-free-energy","display_name":"Gibbs free energy","score":0.8476337790489197},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5676122307777405},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5060173869132996},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.4855784773826599},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.42928218841552734},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3707095980644226},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3460378646850586},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.2429494559764862},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.1632070541381836},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15060311555862427},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12586495280265808},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09444358944892883},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08032932877540588}],"concepts":[{"id":"https://openalex.org/C146477669","wikidata":"https://www.wikidata.org/wiki/Q334631","display_name":"Gibbs free energy","level":2,"score":0.8476337790489197},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5676122307777405},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5060173869132996},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.4855784773826599},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.42928218841552734},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3707095980644226},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3460378646850586},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.2429494559764862},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.1632070541381836},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15060311555862427},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12586495280265808},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09444358944892883},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08032932877540588}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1009448","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009448","pdf_url":null,"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:34570771","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34570771","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:56f09c81520b41be9a31771d1666e17a","is_oa":true,"landing_page_url":"https://doaj.org/article/56f09c81520b41be9a31771d1666e17a","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 17, Iss 9, p e1009448 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7389100","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8496854","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:osti.gov:1822497","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1822497","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1824882","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1824882","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1903905","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1903905","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8496854","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8496854","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.1009448","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009448","pdf_url":null,"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":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8399999737739563}],"awards":[{"id":"https://openalex.org/G1433376465","display_name":null,"funder_award_id":"2019897","funder_id":"https://openalex.org/F4320332169","funder_display_name":"Directorate for Computer and Information Science and Engineering"},{"id":"https://openalex.org/G1489425746","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1637692498","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1645119126","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1719536385","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2063335192","display_name":"Molecule Maker Lab Institute (MMLI): An AI Institute for Molecular Discovery, Synthetic Strategy, and Manufacturing","funder_award_id":"2019897","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3121793570","display_name":null,"funder_award_id":"00OR22725","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G4661815001","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320337801","funder_display_name":"Center for Bioenergy Innovation"},{"id":"https://openalex.org/G6495930337","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7252128611","display_name":null,"funder_award_id":"2019897","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G7995982022","display_name":null,"funder_award_id":"DE-AC05","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8269158468","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8906985441","display_name":null,"funder_award_id":"00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332169","display_name":"Directorate for Computer and Information Science and Engineering","ror":"https://ror.org/025kzpk63"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320337801","display_name":"Center for Bioenergy Innovation","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W1009215777","https://openalex.org/W1508604947","https://openalex.org/W1528140509","https://openalex.org/W1563380435","https://openalex.org/W1593014412","https://openalex.org/W1601795611","https://openalex.org/W1605708511","https://openalex.org/W1663973292","https://openalex.org/W1952732684","https://openalex.org/W1978119727","https://openalex.org/W1992043510","https://openalex.org/W1997733142","https://openalex.org/W1999912067","https://openalex.org/W2006661775","https://openalex.org/W2007750874","https://openalex.org/W2015449517","https://openalex.org/W2017300528","https://openalex.org/W2021733365","https://openalex.org/W2026559278","https://openalex.org/W2042067428","https://openalex.org/W2051434435","https://openalex.org/W2067156145","https://openalex.org/W2079114878","https://openalex.org/W2083527495","https://openalex.org/W2091085232","https://openalex.org/W2116802060","https://openalex.org/W2116976883","https://openalex.org/W2123015215","https://openalex.org/W2125122419","https://openalex.org/W2135900956","https://openalex.org/W2141067619","https://openalex.org/W2154126596","https://openalex.org/W2164904971","https://openalex.org/W2173027866","https://openalex.org/W2315454599","https://openalex.org/W2471639121","https://openalex.org/W2558229157","https://openalex.org/W2559588208","https://openalex.org/W2622206241","https://openalex.org/W2736080104","https://openalex.org/W2747416722","https://openalex.org/W2768490449","https://openalex.org/W2777639606","https://openalex.org/W2782584560","https://openalex.org/W2796322979","https://openalex.org/W2800160465","https://openalex.org/W2895341279","https://openalex.org/W2898189477","https://openalex.org/W2902840690","https://openalex.org/W2903889880","https://openalex.org/W2906587988","https://openalex.org/W2917082012","https://openalex.org/W2938072319","https://openalex.org/W2949078105","https://openalex.org/W2951700574","https://openalex.org/W2952823365","https://openalex.org/W2953806552","https://openalex.org/W2964113829","https://openalex.org/W3016443908","https://openalex.org/W3020638658","https://openalex.org/W3093734399","https://openalex.org/W3104098743","https://openalex.org/W4238532985","https://openalex.org/W4253533330","https://openalex.org/W4298563669","https://openalex.org/W6678209754"],"related_works":["https://openalex.org/W2255699127","https://openalex.org/W2364598349","https://openalex.org/W2317273365","https://openalex.org/W1984013971","https://openalex.org/W2505786821","https://openalex.org/W2379022087","https://openalex.org/W1965596400","https://openalex.org/W4386032686","https://openalex.org/W1990776955","https://openalex.org/W2013704760"],"abstract_inverted_index":{"Group":[0],"contribution":[1],"(GC)":[2],"methods":[3,30,86],"are":[4,31],"conventionally":[5],"used":[6],"in":[7],"thermodynamics":[8],"analysis":[9,59],"of":[10,21,67,136,175],"metabolic":[11,124],"pathways":[12],"to":[13,42,47,83,109,146,154],"estimate":[14],"the":[15,65,111,134,156],"standard":[16,157],"Gibbs":[17,90,112,158],"energy":[18,91,113,159],"change":[19,114,160],"(\u0394rG'o)":[20],"enzymatic":[22],"reactions":[23,117,162],"from":[24],"limited":[25,32],"experimental":[26],"measurements.":[27],"However,":[28],"these":[29],"by":[33],"their":[34],"dependence":[35],"on":[36],"manually":[37],"curated":[38],"groups":[39],"and":[40,72,87,95,118,166,181],"inability":[41],"capture":[43,89],"stereochemical":[44],"information,":[45],"leading":[46],"low":[48],"reaction":[49,75,137],"coverage.":[50,76],"Herein,":[51],"we":[52,148],"introduce":[53],"an":[54],"automated":[55],"molecular":[56],"fingerprint-based":[57],"thermodynamic":[58],"tool":[60,170],"called":[61],"dGPredictor":[62,77],"that":[63],"enables":[64],"consideration":[66],"stereochemistry":[68],"within":[69,121],"metabolite":[70],"structures":[71],"thus":[73],"increases":[74],"has":[78],"comparable":[79],"prediction":[80],"accuracy":[81],"compared":[82],"existing":[84],"GC":[85],"can":[88],"changes":[92],"for":[93,115,131,161],"isomerase":[94],"transferase":[96],"reactions,":[97],"which":[98],"exhibit":[99],"no":[100],"overall":[101],"group":[102],"changes.":[103],"We":[104],"also":[105],"demonstrate":[106],"dGPredictor's":[107],"ability":[108],"predict":[110,155],"novel":[116,182],"seamless":[119],"integration":[120],"de":[122],"novo":[123],"pathway":[125],"design":[126],"tools":[127],"such":[128],"as":[129,178,184],"novoStoic":[130],"safeguarding":[132],"against":[133],"inclusion":[135],"steps":[138],"with":[139],"infeasible":[140],"directionalities.":[141],"To":[142],"facilitate":[143],"easy":[144],"access":[145],"dGPredictor,":[147],"developed":[149],"a":[150],"graphical":[151],"user":[152,173],"interface":[153],"at":[163],"various":[164],"pH":[165],"ionic":[167],"strengths.":[168],"The":[169],"allows":[171],"customized":[172],"input":[174],"known":[176],"metabolites":[177,183],"KEGG":[179],"IDs":[180],"InChI":[185],"strings":[186],"(https://github.com/maranasgroup/dGPredictor).":[187]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}
