Atomevo: a web server combining protein modelling, docking, molecular dynamic simulation and MMPBSA analysis of Candida antarctica lipase B (CalB) fusion protein

• Published in: Bioresources and Bioprocessing
• Main Authors: Jin-Heng Hao, Dun-Jin Zheng, Yu-Hao Ye, Jie-Ting Yu, Xin-Yao Li, Mei-Jie Xiong, Wen-Hao Jiang, Kang-Ping He, Pei-Yu Li, Yong-Si Lv, Wei-Ming Gu, Lin-Hao Lai, Yi-Da Wu, Shi-Lin Cao
• Format: Article in Journal/Newspaper
• Language: English
• Published: SpringerOpen 2022
• Subjects: Biofuel; Molecular dynamics simulation; Docking; MMPBSA; Web Server; Technology; T; Chemical technology; TP1-1185; Biotechnology; TP248.13-248.65; Vina; Antarc*; Antarctica
• Online Access: https://doi.org/10.1186/s40643-022-00546-y; https://doaj.org/article/bf8e7f268ce94528a4788974d2926533

Abstract Although current computational biology software is available and has prompted the development of enzyme–substrates simulation, they are difficult to install and inconvenient to use. This makes the time-consuming and error-prone process. By far there is still a lack of a complete tool which can provide a one-stop service for the enzyme–substrates simulation process. Hence, in this study, several computational biology software was extended development and integrated as a website toolbox named Atomevo. The Atomevo is a free web server providing a user-friendly interface for enzyme–substrates simulation: (1) protein homologous modeling; (2) parallel docking module of Autodock Vina 1.2; (3) automatic modeling builder for Gromacs molecular dynamics simulation package; and (4) Molecular Mechanics/Poisson–Boltzmann Surface Area (MMPBSA) analysis module for receptor–ligand binding affinity analysis. We officially launched the web server and provided instructions through a case for the design and simulation of Candida antarctica lipase B (CalB) fusion protein called Maltose Binding Protein—Thioredoxin A—Candida antarctica lipase B (MBP-TrxA-CalB). Graphical Abstract