Abstract：
Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.
摘要：
酶是许多应用的流行催化剂，尤其是在工业中。生物催化剂的大规模使用面临着一些限制，如运行稳定性低，低可回收性，酶成本高。酶固定化是解决这些问题的有益策略。生物信息学工具通常可以正确预测固定结果，从而以最少的时间消耗成本有效的实验阶段。本研究通过对截至2022年12月11日的已发表文章的全面系统回顾，提供了预测固定化过程的计算机方法概述。它还提到了过程的优缺点，并解释了固定评估所需的每种方法的计算分析。在这方面,筛选了WebofScience和Scopus数据库以获得相关出版物。筛选收集的文件后（n=3873），选择了60篇文章进行审查。所选的论文已应用于计算机程序，包括仅分子动力学（MD）模拟（n=20），平行回火蒙特卡罗(PTMC)和MD模拟(n=3)，MD和对接（n=1），密度泛函理论(DFT)和MD(n=1)，仅对接（n=11），金属离子结合位点预测(MIB)服务器和对接(n=2)，对接和DFT(n=1)，酶表面的对接和分析(n=1)，只有DFT（n=1），只有MIB服务器（n=2），酶结构和表面分析(n=12)，固定衍生物的合理设计(RDID)软件(n=3)，和耗散粒子动力学(DPD；n=2)。在大多数纳入研究(n=51)中，除计算机评估外，还对酶的固定化进行了实验研究。
