{"id":"https://openalex.org/W2754362260","doi":"https://doi.org/10.1186/s13321-017-0239-6","title":"A review of parameters and heuristics for guiding metabolic pathfinding","display_name":"A review of parameters and heuristics for guiding metabolic pathfinding","publication_year":2017,"publication_date":"2017-09-15","ids":{"openalex":"https://openalex.org/W2754362260","doi":"https://doi.org/10.1186/s13321-017-0239-6","mag":"2754362260","pmid":"https://pubmed.ncbi.nlm.nih.gov/29086092"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-017-0239-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-017-0239-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-017-0239-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-017-0239-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070262342","display_name":"Sarah M. Kim","orcid":"https://orcid.org/0000-0001-7627-1489"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah M. Kim","raw_affiliation_strings":["Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA"],"raw_orcid":"https://orcid.org/0000-0001-7627-1489","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102729808","display_name":"Matthew I. Pe\u00f1a","orcid":"https://orcid.org/0000-0002-4322-7462"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew I. Pe\u00f1a","raw_affiliation_strings":["Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061397940","display_name":"Mark Moll","orcid":"https://orcid.org/0000-0002-0451-2797"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Moll","raw_affiliation_strings":["Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038858646","display_name":"George N. Bennett","orcid":"https://orcid.org/0000-0003-1408-8915"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"George N. Bennett","raw_affiliation_strings":["Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lydia E. Kavraki","raw_affiliation_strings":["Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA. kavraki@rice.edu","Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA. kavraki@rice.edu","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5067205988"],"corresponding_institution_ids":["https://openalex.org/I74775410"],"apc_list":{"value":2390,"currency":"USD","value_usd":2390},"apc_paid":{"value":2390,"currency":"USD","value_usd":2390},"fwci":1.9672,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.86849869,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"51","last_page":"51"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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":0.9998999834060669,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pathfinding","display_name":"Pathfinding","score":0.9491884708404541},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6894822120666504},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.6693669557571411},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.4793049395084381},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.4187558889389038},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3204440474510193},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18687212467193604},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.12262481451034546},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07184487581253052}],"concepts":[{"id":"https://openalex.org/C25321074","wikidata":"https://www.wikidata.org/wiki/Q1969601","display_name":"Pathfinding","level":4,"score":0.9491884708404541},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6894822120666504},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.6693669557571411},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.4793049395084381},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.4187558889389038},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3204440474510193},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18687212467193604},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.12262481451034546},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07184487581253052},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.0},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.0},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-017-0239-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-017-0239-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-017-0239-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:29086092","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29086092","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 cheminformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:4536769","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5602787","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:9fcc90dd6a17474c95fd8ad9a2a8c04a","is_oa":true,"landing_page_url":"https://doaj.org/article/9fcc90dd6a17474c95fd8ad9a2a8c04a","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":"Journal of Cheminformatics, Vol 9, Iss 1, Pp 1-13 (2017)","raw_type":"article"},{"id":"pmh:oai:repository.rice.edu:1911/97390","is_oa":true,"landing_page_url":"http://doi.org/10.1186/s13321-017-0239-6.","pdf_url":null,"source":{"id":"https://openalex.org/S4306401268","display_name":"Rice Digital Scholarship Archive (Rice University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74775410","host_organization_name":"Rice University","host_organization_lineage":["https://openalex.org/I74775410"],"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":null,"raw_type":"Journal article"},{"id":"pmh:oai:scholarship.rice.edu:1911/97390","is_oa":true,"landing_page_url":"http://hdl.handle.net/1911/97390","pdf_url":null,"source":{"id":"https://openalex.org/S4306401268","display_name":"Rice Digital Scholarship Archive (Rice University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74775410","host_organization_name":"Rice University","host_organization_lineage":["https://openalex.org/I74775410"],"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":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/s13321-017-0239-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-017-0239-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-017-0239-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G1722617043","display_name":null,"funder_award_id":"NLM Grant T15 LM007093","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2640905883","display_name":null,"funder_award_id":"T15LM007093","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G4474229680","display_name":"ABI Innovation: Mining Metabolic and Enzyme Databases for the Composition of Non-Canonical Pathways","funder_award_id":"1262491","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6209644326","display_name":"Graduate Research Fellowship Program (GRFP)","funder_award_id":"1450681","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8451205532","display_name":"NLM Training Program in Biomedical Informatics & Data Science for Predoctoral and Postdoctoral Fellows","funder_award_id":"3t15lm007093-26s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2754362260.pdf","grobid_xml":"https://content.openalex.org/works/W2754362260.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W1530729104","https://openalex.org/W1577825084","https://openalex.org/W1598572316","https://openalex.org/W1690472431","https://openalex.org/W1906875694","https://openalex.org/W1934481644","https://openalex.org/W1976672440","https://openalex.org/W1979537657","https://openalex.org/W1983202741","https://openalex.org/W1990226486","https://openalex.org/W1997996256","https://openalex.org/W2021688572","https://openalex.org/W2025060809","https://openalex.org/W2028603053","https://openalex.org/W2029058413","https://openalex.org/W2030555543","https://openalex.org/W2033377040","https://openalex.org/W2058141842","https://openalex.org/W2067156145","https://openalex.org/W2068526246","https://openalex.org/W2075846943","https://openalex.org/W2083527495","https://openalex.org/W2089121522","https://openalex.org/W2092448217","https://openalex.org/W2092899907","https://openalex.org/W2093241068","https://openalex.org/W2097032746","https://openalex.org/W2102850238","https://openalex.org/W2103708054","https://openalex.org/W2104619491","https://openalex.org/W2108859156","https://openalex.org/W2111796963","https://openalex.org/W2112101310","https://openalex.org/W2113531097","https://openalex.org/W2113816218","https://openalex.org/W2116007667","https://openalex.org/W2120550036","https://openalex.org/W2122410182","https://openalex.org/W2123402141","https://openalex.org/W2128601422","https://openalex.org/W2129014750","https://openalex.org/W2129106849","https://openalex.org/W2129860041","https://openalex.org/W2131504364","https://openalex.org/W2135206190","https://openalex.org/W2137450588","https://openalex.org/W2145218967","https://openalex.org/W2146651144","https://openalex.org/W2151697120","https://openalex.org/W2152776677","https://openalex.org/W2163480486","https://openalex.org/W2163898101","https://openalex.org/W2164538999","https://openalex.org/W2165612309","https://openalex.org/W2166323054","https://openalex.org/W2167539386","https://openalex.org/W2168504993","https://openalex.org/W2169517653","https://openalex.org/W2171079088","https://openalex.org/W2181121096","https://openalex.org/W2190425105","https://openalex.org/W2292308161","https://openalex.org/W2297764176","https://openalex.org/W2344676116","https://openalex.org/W2466795701","https://openalex.org/W2471639121","https://openalex.org/W2534303219","https://openalex.org/W2559588208","https://openalex.org/W2569419820","https://openalex.org/W2623293810","https://openalex.org/W4298226842"],"related_works":["https://openalex.org/W385704401","https://openalex.org/W3043436041","https://openalex.org/W1990088060","https://openalex.org/W2352726313","https://openalex.org/W2947043338","https://openalex.org/W3197240279","https://openalex.org/W2146372898","https://openalex.org/W2969524935","https://openalex.org/W4292686787","https://openalex.org/W1971080541"],"abstract_inverted_index":{"Recent":[0],"developments":[1],"in":[2,32,53,70,117,139],"metabolic":[3,71,86,95,123,151,164,218],"engineering":[4,72,219],"have":[5,74],"led":[6],"to":[7,59,113,135,175,199],"the":[8,16,19,38,43,89,99,111,118,130,137,150,173,180,203],"successful":[9],"biosynthesis":[10,67],"of":[11,18,40,82,93,101,122,160,205,228],"valuable":[12,57],"products,":[13],"such":[14],"as":[15,172,183],"precursor":[17],"antimalarial":[20],"compound,":[21],"artemisinin,":[22],"and":[23,46,52,62,85,132,145,158,186,192,212],"opioid":[24],"precursor,":[25],"thebaine.":[26],"Synthesizing":[27],"these":[28,56,214,229],"traditionally":[29],"plant-derived":[30],"compounds":[31,58],"genetically":[33],"modified":[34],"yeast":[35],"cells":[36],"introduces":[37],"possibility":[39],"significantly":[41],"reducing":[42],"total":[44],"time":[45,116],"resources":[47],"required":[48],"for":[49,104,178,208,224],"their":[50],"production,":[51],"turn,":[54],"allows":[55],"become":[60,200],"cheaper":[61],"more":[63,201],"readily":[64],"available.":[65],"Most":[66],"pathways":[68],"used":[69,134],"applications":[73],"been":[75],"discovered":[76],"manually,":[77],"requiring":[78],"a":[79],"tedious":[80],"search":[81,138,168],"existing":[83,217],"literature":[84],"databases.":[87],"However,":[88],"recent":[90,140],"rapid":[91],"development":[92,100,204],"available":[94],"information":[96,148],"has":[97,110,188],"enabled":[98],"automated":[102],"approaches":[103,197],"identifying":[105],"novel":[106],"pathways.":[107,161],"Computer-assisted":[108],"pathfinding":[109,141,165,181,196,230],"potential":[112],"save":[114],"biochemists":[115],"initial":[119],"discovery":[120],"steps":[121],"engineering.":[124],"In":[125],"this":[126],"paper,":[127],"we":[128],"review":[129],"parameters":[131,144],"heuristics":[133,146],"guide":[136],"algorithms.":[142],"These":[143],"capture":[147],"on":[149],"network":[152],"structure,":[153],"compound":[154],"structures,":[155],"reaction":[156],"features,":[157],"organism-specificity":[159],"No":[162],"one":[163],"algorithm":[166],"or":[167],"parameter":[169,187],"stands":[170],"out":[171],"best":[174],"use":[176,227],"broadly":[177],"solving":[179],"problem,":[182],"each":[184],"method":[185],"its":[189],"own":[190],"strengths":[191],"shortcomings.":[193],"As":[194],"assisted":[195],"continue":[198],"sophisticated,":[202],"better":[206],"methods":[207],"visualizing":[209],"pathway":[210],"results":[211,215],"integrating":[213],"into":[216],"practices":[220],"is":[221],"also":[222],"important":[223],"encouraging":[225],"wider":[226],"methods.":[231]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
