{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T19:45:05Z","timestamp":1793130305705,"version":"4.5.0"},"reference-count":33,"publisher":"Elsevier BV","issue":"15","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T00:00:00Z","timestamp":1739404800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["1844"],"award-info":[{"award-number":["1844"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["815379"],"award-info":[{"award-number":["815379"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["101140394"],"award-info":[{"award-number":["101140394"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001663","name":"Volkswagen Foundation","doi-asserted-by":"publisher","award":["94747"],"award-info":[{"award-number":["94747"]}],"id":[{"id":"10.13039\/501100001663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018703","name":"European Innovation Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018703","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Biology"],"published-print":{"date-parts":[[2025,8]]},"DOI":"10.1016\/j.jmb.2025.169011","type":"journal-article","created":{"date-parts":[[2025,2,15]],"date-time":"2025-02-15T17:01:49Z","timestamp":1739638909000},"page":"169011","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"title":["htFuncLib: Designing Libraries of Active-site Multipoint Mutants for Protein Optimization"],"prefix":"10.1016","volume":"437","author":[{"given":"Rosalie","family":"Lipsh-Sokolik","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarel J.","family":"Fleishman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmb.2025.169011_b0005","doi-asserted-by":"crossref","DOI":"10.1155\/2014\/572409","article-title":"Local packing density is the main structural determinant of the rate of protein sequence evolution at site level","volume":"2014","author":"Yeh","year":"2014","journal-title":"Biomed Res. Int."},{"key":"10.1016\/j.jmb.2025.169011_b0010","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1002\/prot.25034","article-title":"Dissecting the roles of local packing density and longer-range effects in protein sequence evolution: Protein Sequence Evolution","volume":"84","author":"Shahmoradi","year":"2016","journal-title":"Proteins"},{"key":"10.1016\/j.jmb.2025.169011_b0015","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1002\/pro.2897","article-title":"Epistasis in protein evolution","volume":"25","author":"Starr","year":"2016","journal-title":"Protein Sci."},{"key":"10.1016\/j.jmb.2025.169011_b0020","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.tig.2014.09.009","article-title":"Topological features of rugged fitness landscapes in sequence space","volume":"31","author":"Kondrashov","year":"2015","journal-title":"Trends Genet."},{"key":"10.1016\/j.jmb.2025.169011_b0025","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/nature05451","article-title":"Empirical fitness landscapes reveal accessible evolutionary paths","volume":"445","author":"Poelwijk","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2025.169011_b0030","article-title":"Evolutionary paths that link orthogonal pairs of binding proteins","author":"Avizemer","year":"2023","journal-title":"Res. Sq."},{"key":"10.1016\/j.jmb.2025.169011_b0035","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.jtbi.2010.12.015","article-title":"Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes","volume":"272","author":"Poelwijk","year":"2011","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.jmb.2025.169011_b0040","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1038\/nature09105","article-title":"Sequence space and the ongoing expansion of the protein universe","volume":"465","author":"Povolotskaya","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2025.169011_b0045","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1002\/pro.2876","article-title":"How mutational epistasis impairs predictability in protein evolution and design","volume":"25","author":"Miton","year":"2016","journal-title":"Protein Sci."},{"key":"10.1016\/j.jmb.2025.169011_b0050","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2025.169011_b0055","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-023-06415-8","article-title":"De novo design of protein structure and function with RFdiffusion","author":"Watson","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2025.169011_b0060","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1126\/science.add2187","article-title":"Robust deep learning\u2013based protein sequence design using ProteinMPNN","volume":"378","author":"Dauparas","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.jmb.2025.169011_b0065","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2314999121","article-title":"Addressing epistasis in the design of protein function","volume":"121","author":"Lipsh-Sokolik","year":"2024","journal-title":"PNAS"},{"key":"10.1016\/j.jmb.2025.169011_b0070","doi-asserted-by":"crossref","DOI":"10.1021\/acscentsci.3c01275","article-title":"Opportunities and challenges for machine learning-assisted enzyme engineering","author":"Yang","year":"2024","journal-title":"ACS Cent. Sci."},{"key":"10.1016\/j.jmb.2025.169011_b0075","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.molcel.2018.08.033","article-title":"Automated design of efficient and functionally diverse enzyme repertoires","volume":"72","author":"Khersonsky","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2025.169011_b0080","article-title":"Accelerating enzyme discovery and engineering with high-throughput screening","author":"Bozkurt","year":"2024","journal-title":"Nature Prod. Rep."},{"key":"10.1016\/j.jmb.2025.169011_b0085","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1126\/science.ade9434","article-title":"Combinatorial assembly and design of enzymes","volume":"379","author":"Lipsh-Sokolik","year":"2023","journal-title":"Science"},{"key":"10.1016\/j.jmb.2025.169011_b0090","doi-asserted-by":"crossref","first-page":"2890","DOI":"10.1038\/s41467-023-38099-z","article-title":"Designed active-site library reveals thousands of functional GFP variants","volume":"14","author":"Weinstein","year":"2023","journal-title":"Nature Commun."},{"key":"10.1016\/j.jmb.2025.169011_b0095","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.1021\/acs.jctc.7b00125","article-title":"The Rosetta all-atom energy function for macromolecular modeling and design","volume":"13","author":"Alford","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/j.jmb.2025.169011_b0100","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2022012118","article-title":"Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrant Pseudomonas aeruginosa biofilms","volume":"118","author":"VanDrisse","year":"2021","journal-title":"PNAS"},{"key":"10.1016\/j.jmb.2025.169011_b0105","article-title":"A computationally designed panel of diverse and selective peroxygenases for terpene oxyfunctionalization","author":"M\u00fcnch","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.jmb.2025.169011_b0110","doi-asserted-by":"crossref","first-page":"5554","DOI":"10.1002\/anie.202014239","article-title":"Engineered enzymes enable selective N-alkylation of pyrazoles with simple haloalkanes","volume":"60","author":"Bengel","year":"2021","journal-title":"Angew. Chem. Int. Ed Engl."},{"key":"10.1016\/j.jmb.2025.169011_b0115","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s13068-024-02478-5","article-title":"In silico design of multipoint mutants for enhanced performance of Thermomyces lanuginosus lipase for efficient biodiesel production","volume":"17","author":"Huang","year":"2024","journal-title":"Biotechnol. Biofuels Bioprod."},{"key":"10.1016\/j.jmb.2025.169011_b0120","doi-asserted-by":"crossref","first-page":"13164","DOI":"10.1021\/acscatal.2c03006","article-title":"Designed high-redox potential laccases exhibit high functional diversity","volume":"12","author":"Barber-Zucker","year":"2022","journal-title":"ACS Catal."},{"key":"10.1016\/j.jmb.2025.169011_b0125","doi-asserted-by":"crossref","first-page":"e4400","DOI":"10.1002\/pro.4400","article-title":"Assessing and enhancing foldability in designed proteins","volume":"31","author":"Listov","year":"2022","journal-title":"Protein Sci."},{"key":"10.1016\/j.jmb.2025.169011_b0130","article-title":"High-efficiency Kemp eliminases by complete computational design","author":"Listov","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.jmb.2025.169011_b0135","doi-asserted-by":"crossref","DOI":"10.1021\/jacs.2c11118","article-title":"Repertoire of computationally designed peroxygenases for enantiodivergent C-H oxyfunctionalization reactions","author":"Gomez de Santos","year":"2023","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.jmb.2025.169011_b0140","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007207","article-title":"Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces","volume":"15","author":"Warszawski","year":"2019","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jmb.2025.169011_b0145","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2021.167099","article-title":"Biomolecular recognition of the glycan neoantigen CA19-9 by distinct antibodies","volume":"433","author":"Borenstein-Katz","year":"2021","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2025.169011_b0150","doi-asserted-by":"crossref","first-page":"5286","DOI":"10.1038\/s41467-018-07722-9","article-title":"Ultrahigh specificity in a network of computationally designed protein-interaction pairs","volume":"9","author":"Netzer","year":"2018","journal-title":"Nature Commun."},{"key":"10.1016\/j.jmb.2025.169011_b0155","doi-asserted-by":"crossref","first-page":"1","DOI":"10.34133\/2022\/9787581","article-title":"What have we learned from design of function in large proteins?","volume":"2022","author":"Khersonsky","year":"2022","journal-title":"BioDesign Res."},{"key":"10.1016\/j.jmb.2025.169011_b0160","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41580-024-00718-y","article-title":"Opportunities and challenges in design and optimization of protein function","volume":"25","author":"Listov","year":"2024","journal-title":"Nature Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jmb.2025.169011_b0165","doi-asserted-by":"crossref","first-page":"e5169","DOI":"10.1002\/pro.5169","article-title":"GGAssembler: precise and economical design and synthesis of combinatorial mutation libraries","volume":"33","author":"Hoch","year":"2024","journal-title":"Protein Sci."}],"container-title":["Journal of Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283625000774?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283625000774?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T03:58:32Z","timestamp":1777694312000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022283625000774"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":33,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2025,8]]}},"alternative-id":["S0022283625000774"],"URL":"https:\/\/doi.org\/10.1016\/j.jmb.2025.169011","relation":{},"ISSN":["0022-2836"],"issn-type":[{"value":"0022-2836","type":"print"}],"subject":[],"published":{"date-parts":[[2025,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"htFuncLib: Designing Libraries of Active-site Multipoint Mutants for Protein Optimization","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmb.2025.169011","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"simple-article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"169011"}}