DIProT:A deep learning based interactive toolkit for efficient and effective Protein design  

作　　者：Jieling He Wenxu Wu Xiaowo Wang 

机构地区：[1]Ministry of Education Key Laboratory of Bioinformatics,Center for Synthetic and Systems Biology,Bioinformatics Division,Beijing National Research Center for Information Science and Technology,Department of Automation,Tsinghua University,Beijing,China

出　　处：《Synthetic and Systems Biotechnology》2024年第2期217-222,共6页合成和系统生物技术（英文）

基　　金：This work was supported by the National Natural Science Foundation of China(Nos.62250007,62225307,61721003);a grant from the Guoqiang Institute,Tsinghua University(2021GQG1023).

摘　　要：The protein inverse folding problem,designing amino acid sequences that fold into desired protein structures,is a critical challenge in biological sciences.Despite numerous data-driven and knowledge-driven methods,there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein design.In this paper,we present DIProT,an interactive protein design toolkit.DIProT leverages a non-autoregressive deep generative model to solve the inverse folding problem,combined with a protein structure prediction model.This integration allows users to incorporate prior knowledge into the design process,evaluate designs in silico,and form a virtual design loop with human feedback.Our inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets,with promising sequence recovery and inference time.Case studies further illustrate how DIProT can facilitate user-guided protein design.

关 键 词：Computational Protein design Interactive design toolkit Protein inverse folding Non-autoregressive decoding 

分 类 号：Q51[生物学—生物化学]