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@article{2377419,
author = {Khan, Rayyan Tariq and Musil, Miloš and Dvorský, Jan and Damborský, Jiří and Bednář, David},
article_number = {2},
doi = {http://dx.doi.org/10.1002/cpz1.30},
keywords = {ancestral sequence reconstruction; automation; protein engineering; protein evolution; thermostability},
language = {eng},
issn = {2691-1299},
journal = {Current Protocols},
title = {Fully Automated Ancestral Sequence Reconstruction using FireProtASR},
url = {https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.30},
volume = {1},
year = {2021}
}
TY - JOUR
ID - 2377419
AU - Khan, Rayyan Tariq - Musil, Miloš - Dvorský, Jan - Damborský, Jiří - Bednář, David
PY - 2021
TI - Fully Automated Ancestral Sequence Reconstruction using FireProtASR
JF - Current Protocols
VL - 1
IS - 2
PB - Wiley
SN - 26911299
KW - ancestral sequence reconstruction
KW - automation
KW - protein engineering
KW - protein evolution
KW - thermostability
UR - https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.30
N2 - Protein evolution and protein engineering techniques are of great interest in basic science and industrial applications such as pharmacology, medicine, or biotechnology. Ancestral sequence reconstruction (ASR) is a powerful technique for probing evolutionary relationships and engineering robust proteins with good thermostability and broad substrate specificity. The following protocol describes the setting up and execution of an automated FireProtASR workflow using a dedicated web site. The service allows for inference of ancestral proteins automatically, from a single protein sequence. Once a protein sequence is submitted, the server will build a dataset of homology sequences, perform a multiple sequence alignment (MSA), build a phylogenetic tree, and reconstruct ancestral nodes. The protocol is also highly flexible and allows for multiple forms of input, advanced settings, and the ability to start jobs from: (i) a single sequence, (ii) a set of homologous sequences, (iii) an MSA, and (iv) a phylogenetic tree. This approach automates all necessary steps and offers a way for novices with limited exposure to ASR techniques to improve the properties of a protein of interest. The technique can even be used to introduce catalytic promiscuity into an enzyme. A web server for accessing the fully automated workflow is freely accessible at https://loschmidt.chemi.muni.cz/fireprotasr/.
ER -
KHAN, Rayyan Tariq, Miloš MUSIL, Jan DVORSKÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. Fully Automated Ancestral Sequence Reconstruction using FireProtASR. \textit{Current Protocols}. Wiley, 2021, vol.~1, No~2. ISSN~2691-1299. Available from: https://dx.doi.org/10.1002/cpz1.30.
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