In:
Bioresources and Bioprocessing, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2022-12)
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
Type of Medium:
Online Resource
ISSN:
2197-4365
DOI:
10.1186/s40643-022-00546-y
Language:
English
Publisher:
Springer Science and Business Media LLC
Publication Date:
2022
detail.hit.zdb_id:
2785482-6
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