{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T16:05:29Z","timestamp":1789833929792,"version":"4.0.1"},"reference-count":48,"publisher":"Elsevier","isbn-type":[{"value":"9780443413858","type":"print"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1016\/bs.apcsb.2026.08.013","type":"book-chapter","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T11:37:04Z","timestamp":1787657824000},"page":"383-439","source":"Crossref","is-referenced-by-count":0,"title":["Computational methods for alternative proteins"],"prefix":"10.1016","author":[{"given":"S","family":"Vyshnav","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vino","family":"Sundararajan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajitha Lulu","family":"Sudhakaran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/bs.apcsb.2026.08.013_bib1","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1038\/s41592-019-0598-1","article-title":"Unified rational protein engineering with sequence-based deep representation learning","volume":"16","author":"Alley","year":"2019","journal-title":"Nature Methods"},{"issue":"4","key":"10.1016\/bs.apcsb.2026.08.013_bib2","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.cels.2019.03.006","article-title":"End-to-end differentiable learning of protein structure","volume":"8","author":"AlQuraishi","year":"2019","journal-title":"Cell Systems"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib3","first-page":"7505","article-title":"Generative modeling for protein structures","volume":"31","author":"Anand","year":"2018","journal-title":"Advances in Neural Information Processing Systems"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib4","doi-asserted-by":"crossref","first-page":"4143","DOI":"10.1002\/anie.201708408","article-title":"Directed evolution: Bringing new chemistry to life","volume":"57","author":"Arnold","year":"2018","journal-title":"Angewandte Chemie International Edition"},{"issue":"6557","key":"10.1016\/bs.apcsb.2026.08.013_bib5","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science (New York, N. Y.)"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib6","first-page":"181","article-title":"Prospectus of cultured meat","volume":"10","author":"Bhat","year":"2011","journal-title":"Comprehensive Reviews in Food Science and Food Safety"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib7","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/s41592-021-01100-y","article-title":"Low-N protein engineering with data-efficient deep learning","volume":"18","author":"Biswas","year":"2021","journal-title":"Nature Methods"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib8","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.tifs.2012.07.002","article-title":"The future supply of animal-derived protein","volume":"29","author":"Boland","year":"2013","journal-title":"Trends in Food Science & Technology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib9","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/nature11117","article-title":"Engineering the third wave of biocatalysis","volume":"485","author":"Bornscheuer","year":"2012","journal-title":"Nature"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib10","article-title":"Consumer acceptance of cultured meat: A systematic review","volume":"89","author":"Bryant","year":"2021","journal-title":"Food Quality and Preference"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib11","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3389\/fnut.2020.00007","article-title":"The myth of cultured meat","volume":"7","author":"Chriki","year":"2020","journal-title":"Frontiers in Nutrition"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib12","first-page":"541","article-title":"Synthetic and systems biology for microbial production","volume":"14","author":"Chubukov","year":"2016","journal-title":"Nature Reviews. Microbiology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib13","article-title":"AI for sustainable future foods","author":"Datta","year":"2025","journal-title":"npj Science of Food"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib14","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.tifs.2018.08.011","article-title":"Structuring processes for meat analogues","volume":"81","author":"Dekkers","year":"2018","journal-title":"Trends in Food Science & Technology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib15","first-page":"3","article-title":"Enzyme engineering by targeted libraries","volume":"580","author":"Goldsmith","year":"2017","journal-title":"Methods in Enzymology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib16","series-title":"Deep learning","author":"Goodfellow","year":"2016"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib17","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev-food-062520-093642","article-title":"Alternative protein sources as technological ingredients","volume":"12","author":"Grossmann","year":"2021","journal-title":"Annual Review of Food Science and Technology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib18","first-page":"171","article-title":"Future protein supply and demand","volume":"66","author":"Henchion","year":"2017","journal-title":"Trends in Food Science & Technology"},{"issue":"6526","key":"10.1016\/bs.apcsb.2026.08.013_bib19","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1126\/science.abd7331","article-title":"Learning the language of viral evolution and escape","volume":"371","author":"Hie","year":"2022","journal-title":"Science (New York, N. Y.)"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib20","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/nature19946","article-title":"The coming of age of de novo protein design","volume":"537","author":"Huang","year":"2016","journal-title":"Nature"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib21","first-page":"15820","article-title":"Generative models for graph-based protein design","volume":"32","author":"Ingraham","year":"2019","journal-title":"Advances in Neural Information Processing Systems"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib22","doi-asserted-by":"crossref","DOI":"10.1016\/j.crfs.2024.100882","article-title":"Alternative proteins for sustainable diets and meat analog production","author":"Jafarzadeh","year":"2024","journal-title":"Current Research in Food Science"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib23","first-page":"1241","article-title":"Meat analogues: Plant-based alternatives","volume":"55","author":"Joshi","year":"2015","journal-title":"Critical Reviews in Food Science and Nutrition"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib24","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with deep learning","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib25","doi-asserted-by":"crossref","DOI":"10.3389\/fsci.2025.1599300","article-title":"Hybrid alternative protein-based foods: Designing sustainable food systems","author":"Kaplan","year":"2025","journal-title":"Frontiers in Science of Food"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib26","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1126\/science.1193990","article-title":"Manufacturing molecules through metabolic engineering","volume":"330","author":"Keasling","year":"2010","journal-title":"Science (New York, N. Y.)"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib27","series-title":"Comprehensive review of alternative proteins in food systems","author":"Klinmalai","year":"2025"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib28","first-page":"7","article-title":"Plant-based meat analogues","volume":"29","author":"Kyriakopoulou","year":"2019","journal-title":"Current Opinion in Food Science"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib29","first-page":"115","article-title":"Systems metabolic engineering of microorganisms","volume":"30","author":"Lee","year":"2012","journal-title":"Nature Biotechnology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib30","first-page":"1","article-title":"Plant protein ingredients with food functionality potential","volume":"31","author":"Loveday","year":"2020","journal-title":"Current Opinion in Food Science"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib31","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-47091-0","article-title":"Alternative protein sources: Science-powered innovations for sustainable food systems","author":"Lurie-Luke","year":"2024","journal-title":"Nature Communications"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib32","series-title":"Protein engineering handbook","author":"Lutz","year":"2009"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib33","doi-asserted-by":"crossref","DOI":"10.1038\/s41538-024-00291-w","article-title":"Current challenges of alternative proteins as future foods","author":"Malila","year":"2024","journal-title":"npj Science of Food"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib34","doi-asserted-by":"crossref","first-page":"11941","DOI":"10.1021\/acs.est.5b01614","article-title":"Anticipatory life cycle analysis of cultured meat","volume":"49","author":"Mattick","year":"2015","journal-title":"Environmental Science & Technology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib35","first-page":"1459","article-title":"Language models enable zero-shot prediction of the effects of mutations on protein function","volume":"18","author":"Meier","year":"2021","journal-title":"Nature Methods"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib36","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1016\/j.cell.2016.02.004","article-title":"Engineering cellular metabolism","volume":"164","author":"Nielsen","year":"2016","journal-title":"Cell"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib37","first-page":"245","article-title":"Engineering synergy in biotechnology","volume":"13","author":"Nielsen","year":"2017","journal-title":"Nature Chemical Biology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib38","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.meatsci.2012.04.008","article-title":"Cultured meat from stem cells","volume":"92","author":"Post","year":"2012","journal-title":"Meat Science"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib39","article-title":"Transformer protein language models are unsupervised structure learners","author":"Rao","year":"2021","journal-title":"International Conference on Learning Representations"},{"issue":"15","key":"10.1016\/bs.apcsb.2026.08.013_bib40","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2016239118","article-title":"Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences","volume":"118","author":"Rives","year":"2021","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib41","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.tifs.2018.04.010","article-title":"Bringing cultured meat to market","volume":"78","author":"Stephens","year":"2018","journal-title":"Trends in Food Science & Technology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib42","article-title":"Computational design of intrinsically disordered proteins","author":"Tesei","year":"2025","journal-title":"Current Opinion in Structural Biology"},{"issue":"6558","key":"10.1016\/bs.apcsb.2026.08.013_bib43","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1126\/science.abe5650","article-title":"Geometric deep learning of RNA structure","volume":"373","author":"Townshend","year":"2021","journal-title":"Science (New York, N. Y.)"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib44","first-page":"47","article-title":"Understanding the future of alternative proteins","volume":"102","author":"Tziva","year":"2020","journal-title":"Trends in Food Science & Technology"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib45","doi-asserted-by":"crossref","first-page":"8852","DOI":"10.1073\/pnas.1901979116","article-title":"Machine learning-assisted directed protein evolution with combinatorial libraries","volume":"116","author":"Wu","year":"2019","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib46","first-page":"2642","article-title":"Learned protein embeddings for machine learning","volume":"34","author":"Yang","year":"2018","journal-title":"Bioinformatics (Oxford, England)"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib47","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/s41592-019-0496-6","article-title":"Machine-learning-guided directed evolution for protein engineering","volume":"16","author":"Yang","year":"2019","journal-title":"Nature Methods"},{"key":"10.1016\/bs.apcsb.2026.08.013_bib48","doi-asserted-by":"crossref","DOI":"10.1016\/j.foodcont.2025.111777","article-title":"Exploring meat analogs: A review of alternative proteins and food safety challenges","author":"Zhao","year":"2026","journal-title":"Food Control"}],"container-title":["Advances in Protein Chemistry and Structural Biology","Alternative Proteins"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S187616232600101X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S187616232600101X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T15:38:30Z","timestamp":1789832310000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S187616232600101X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9780443413858"],"references-count":48,"URL":"https:\/\/doi.org\/10.1016\/bs.apcsb.2026.08.013","relation":{},"ISSN":["1876-1623"],"issn-type":[{"value":"1876-1623","type":"print"}],"subject":[],"published":{"date-parts":[[2026]]}}}