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Advancements in technology emphasize the critical role of designing nanobodies and humanized antibodies in antibody engineering. However, current experimental methods are costly and time-consuming. Computational approaches, while progressing, faced limitations due to insufficient structural data and the absence of a standardized protocol. To tackle these challenges, our lab previously developed IsAb1.0, an in silico antibody design protocol. Yet, IsAb1.0 lacked accuracy, had a complex procedure, and required extensive antibody bioinformation. Moreover, it overlooked nanobody and humanized antibody design, hindering therapeutic antibody development. Building upon IsAb1.0, we enhanced our design protocol with artificial intelligence methods to create IsAb2.0. IsAb2.0 utilized AlphaFold-Multimer (2.3\/3.0) for accurate modeling and complex construction without templates and employed the precise FlexddG method for in silico antibody optimization. Validated through optimization of a humanized nanobody J3 (HuJ3) targeting HIV-1 gp120, IsAb2.0 predicted five mutations that can improve HuJ3-gp120 binding affinity. These predictions were confirmed by commercial software and validated through binding and neutralization assays. IsAb2.0 streamlined antibody design, offering insights into future techniques to accelerate immunotherapy development.<\/jats:p>","DOI":"10.1093\/bib\/bbae445","type":"journal-article","created":{"date-parts":[[2024,9,17]],"date-time":"2024-09-17T17:09:38Z","timestamp":1726592978000},"source":"Crossref","is-referenced-by-count":7,"title":["AI-based IsAb2.0 for antibody design"],"prefix":"10.1093","volume":"25","author":[{"given":"Tianjian","family":"Liang","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences , Computational Chemical Genomics Screening Center, Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy, , 335 Sutherland Drive, Pittsburgh, PA 15261, United States"},{"name":"University of Pittsburgh , Computational Chemical Genomics Screening Center, Pharmacometrics & System Pharmacology PharmacoAnalytics, School of Pharmacy, , 335 Sutherland Drive, Pittsburgh, PA 15261, United States"},{"name":"National Center of Excellence for 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