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AB-Gen:Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning

摘要Antibody leads must fulfill multiple desirable properties to be clinical candidates.Pri-marily due to the low throughput in the experimental procedure,the need for such multi-property optimization causes the bottleneck in preclinical antibody discovery and development,because addressing one issue usually causes another.We developed a reinforcement learning(RL)method,named AB-Gen,for antibody library design using a generative pre-trained transformer(GPT)as the policy network of the RL agent.We showed that this model can learn the antibody space of heavy chain complementarity determining region 3(CDRH3)and generate sequences with similar property distributions.Besides,when using human epidermal growth factor receptor-2(HER2)as the target,the agent model of AB-Gen was able to generate novel CDRH3 sequences that fulfill multi-property constraints.Totally,509 generated sequences were able to pass all prop-erty filters,and three highly conserved residues were identified.The importance of these residues was further demonstrated by molecular dynamics simulations,consolidating that the agent model was capable of grasping important information in this complex optimization task.Overall,the AB-Gen method is able to design novel antibody sequences with an improved success rate than the tra-ditional propose-then-filter approach.It has the potential to be used in practical antibody design,thus empowering the antibody discovery and development process.The source code of AB-Gen is freely available at Zenodo(https://doi.org/10.5281/zenodo.7657016)and BioCode(https://ngdc.cncb.ac.cn/biocode/tools/BT007341).

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作者 Xiaopeng Xu [1] Tiantian Xu [2] Juexiao Zhou [1] Xingyu Liao [1] Ruochi Zhang [3] Yu Wang [3] Lu Zhang [4] Xin Gao [1] 学术成果认领
作者单位 Computational Bioscience Research Center(CBRC),King Abdullah University of Science and Technology,Thuwal 23955-6900,Saudi Arabia [1] State Key Laboratory of Structural Chemistry,Fujian Institute of Research on the Structure of Matter,Chinese Academy of Sciences,Fuzhou 350002,China;University of Chinese Academy of Sciences,Beijing 100049,China [2] Syneron Technology,Guangzhou 510000,China [3] State Key Laboratory of Structural Chemistry,Fujian Institute of Research on the Structure of Matter,Chinese Academy of Sciences,Fuzhou 350002,China;University of Chinese Academy of Sciences,Beijing 100049,China;Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry,Fuzhou 361005,China [4]
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DOI 10.1016/j.gpb.2023.03.004
发布时间 2024-03-22(万方平台首次上网日期,不代表论文的发表时间)
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