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Atomevo: a web server combining protein modelling, docking, molecular dynamic simulation and MMPBSA analysis of Candida antarctica lipase B (CalB) fusion protein.
- Source :
-
Bioresources and bioprocessing [Bioresour Bioprocess] 2022 May 13; Vol. 9 (1), pp. 53. Date of Electronic Publication: 2022 May 13. - Publication Year :
- 2022
-
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).<br /> (© 2022. The Author(s).)
Details
- Language :
- English
- ISSN :
- 2197-4365
- Volume :
- 9
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Bioresources and bioprocessing
- Publication Type :
- Academic Journal
- Accession number :
- 38647745
- Full Text :
- https://doi.org/10.1186/s40643-022-00546-y