{"id":"https://openalex.org/W4409754562","doi":"https://doi.org/10.1038/s43588-025-00788-8","title":"Physics-based modeling in the new era of enzyme engineering","display_name":"Physics-based modeling in the new era of enzyme engineering","publication_year":2025,"publication_date":"2025-04-24","ids":{"openalex":"https://openalex.org/W4409754562","doi":"https://doi.org/10.1038/s43588-025-00788-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/40275092"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-025-00788-8","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00788-8","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12239909","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061799028","display_name":"Christopher Jurich","orcid":"https://orcid.org/0000-0001-6592-7980"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Jurich","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, TN, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059001674","display_name":"Qianzhen Shao","orcid":"https://orcid.org/0000-0002-7787-0966"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qianzhen Shao","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, TN, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072055494","display_name":"Xinchun Ran","orcid":"https://orcid.org/0009-0001-5052-1758"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinchun Ran","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, TN, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055785990","display_name":"Zhongyue Yang","orcid":"https://orcid.org/0000-0003-0395-6617"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I4210162197","display_name":"Vanderbilt Health","ror":"https://ror.org/05grhsk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210162197"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhongyue J. Yang","raw_affiliation_strings":["Center for Structural Biology, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","Data Science Institute, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","Department of Chemistry, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu"],"raw_orcid":"https://orcid.org/0000-0003-0395-6617","affiliations":[{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Data Science Institute, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","institution_ids":["https://openalex.org/I200719446","https://openalex.org/I4210162197"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA. zhongyue.yang@vanderbilt.edu","institution_ids":["https://openalex.org/I200719446","https://openalex.org/I4210162197"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055785990"],"corresponding_institution_ids":["https://openalex.org/I200719446","https://openalex.org/I4210162197"],"apc_list":{"value":11690,"currency":"USD","value_usd":11690},"apc_paid":null,"fwci":9.5855,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.98964443,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"5","issue":"4","first_page":"279","last_page":"291"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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/computer-science","display_name":"Computer science","score":0.3352581858634949}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3352581858634949}],"mesh":[{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1038/s43588-025-00788-8","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00788-8","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:40275092","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40275092","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":"Nature computational science","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12239909","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12239909","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":"Nat Comput Sci","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12239909","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12239909","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":"Nat Comput Sci","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2073199438","display_name":null,"funder_award_id":"R35 GM146982","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2534798042","display_name":null,"funder_award_id":"T32 GM065086","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5498920180","display_name":null,"funder_award_id":"R35GM146982","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6094191857","display_name":null,"funder_award_id":"T32 GM149371","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7448097337","display_name":null,"funder_award_id":"R35GM146982","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":135,"referenced_works":["https://openalex.org/W596730774","https://openalex.org/W1965294699","https://openalex.org/W1979374949","https://openalex.org/W1981075842","https://openalex.org/W1987696643","https://openalex.org/W2008913755","https://openalex.org/W2024872256","https://openalex.org/W2046983748","https://openalex.org/W2049557754","https://openalex.org/W2064719117","https://openalex.org/W2065894452","https://openalex.org/W2074512072","https://openalex.org/W2076820070","https://openalex.org/W2082260955","https://openalex.org/W2097245475","https://openalex.org/W2107025108","https://openalex.org/W2112792893","https://openalex.org/W2114963145","https://openalex.org/W2131003275","https://openalex.org/W2133852950","https://openalex.org/W2134513074","https://openalex.org/W2138992251","https://openalex.org/W2140029897","https://openalex.org/W2143183478","https://openalex.org/W2155871507","https://openalex.org/W2160622786","https://openalex.org/W2164748882","https://openalex.org/W2168009444","https://openalex.org/W2302501749","https://openalex.org/W2334047574","https://openalex.org/W2465687486","https://openalex.org/W2468618868","https://openalex.org/W2521101013","https://openalex.org/W2560598712","https://openalex.org/W2561072227","https://openalex.org/W2602434521","https://openalex.org/W2604678794","https://openalex.org/W2613081940","https://openalex.org/W2621926380","https://openalex.org/W2673359774","https://openalex.org/W2755181646","https://openalex.org/W2768460596","https://openalex.org/W2782741781","https://openalex.org/W2785408708","https://openalex.org/W2789293857","https://openalex.org/W2793869329","https://openalex.org/W2912446381","https://openalex.org/W2942491534","https://openalex.org/W2947457847","https://openalex.org/W2949303384","https://openalex.org/W2952291569","https://openalex.org/W2965286540","https://openalex.org/W2975848503","https://openalex.org/W2981310185","https://openalex.org/W2990862336","https://openalex.org/W2995106228","https://openalex.org/W3002774878","https://openalex.org/W3002870195","https://openalex.org/W3006116138","https://openalex.org/W3014771307","https://openalex.org/W3016672149","https://openalex.org/W3022987161","https://openalex.org/W3041085494","https://openalex.org/W3080100106","https://openalex.org/W3084337575","https://openalex.org/W3088656464","https://openalex.org/W3088927464","https://openalex.org/W3096046766","https://openalex.org/W3102795712","https://openalex.org/W3106395629","https://openalex.org/W3122108845","https://openalex.org/W3137530921","https://openalex.org/W3154916411","https://openalex.org/W3168520514","https://openalex.org/W3168813651","https://openalex.org/W3175582711","https://openalex.org/W3177828909","https://openalex.org/W3193976797","https://openalex.org/W3194166942","https://openalex.org/W3195495531","https://openalex.org/W3196910777","https://openalex.org/W3203085254","https://openalex.org/W3209182025","https://openalex.org/W3215248408","https://openalex.org/W4200187979","https://openalex.org/W4213213574","https://openalex.org/W4214853200","https://openalex.org/W4220669883","https://openalex.org/W4221041249","https://openalex.org/W4223900047","https://openalex.org/W4226363244","https://openalex.org/W4283011713","https://openalex.org/W4292865836","https://openalex.org/W4296032638","https://openalex.org/W4306809720","https://openalex.org/W4307291940","https://openalex.org/W4308780863","https://openalex.org/W4312019699","https://openalex.org/W4320040108","https://openalex.org/W4321099926","https://openalex.org/W4323031658","https://openalex.org/W4328050524","https://openalex.org/W4375853020","https://openalex.org/W4378172157","https://openalex.org/W4382361658","https://openalex.org/W4385477286","https://openalex.org/W4386100532","https://openalex.org/W4386884054","https://openalex.org/W4387693468","https://openalex.org/W4388520183","https://openalex.org/W4388627063","https://openalex.org/W4388971747","https://openalex.org/W4389136677","https://openalex.org/W4389472984","https://openalex.org/W4389608417","https://openalex.org/W4389786948","https://openalex.org/W4390816949","https://openalex.org/W4391999367","https://openalex.org/W4392127821","https://openalex.org/W4392197899","https://openalex.org/W4392659906","https://openalex.org/W4392930582","https://openalex.org/W4394766668","https://openalex.org/W4396637376","https://openalex.org/W4399388315","https://openalex.org/W4399998837","https://openalex.org/W4400026423","https://openalex.org/W4400495967","https://openalex.org/W4401506799","https://openalex.org/W4404105372","https://openalex.org/W4404776863","https://openalex.org/W4407434658","https://openalex.org/W4407448019","https://openalex.org/W4408612813","https://openalex.org/W4409038263"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":15}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
