Detail publikace

Fully Automated Ancestral Sequence Reconstruction using FireProtASR

KHAN, R. MUSIL, M. ŠTOURAČ, J. DAMBORSKÝ, J. BEDNÁŘ, D.

Originální název

Fully Automated Ancestral Sequence Reconstruction using FireProtASR

Typ

článek v časopise ve Scopus, Jsc

Jazyk

angličtina

Originální abstrakt

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/

Klíčová slova

ancestral reconstrution, stable proteins, protein engineering, specificity

Autoři

KHAN, R.; MUSIL, M.; ŠTOURAČ, J.; DAMBORSKÝ, J.; BEDNÁŘ, D.

Vydáno

1. 2. 2021

ISSN

1934-3396

Periodikum

Current Protocols in Bioinformatics

Ročník

1

Číslo

2

Stát

Spojené státy americké

Strany od

1

Strany do

5

Strany počet

5

URL

https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.30

BibTex

@article{BUT168533,
  author="Rayyan {Khan} and Miloš {Musil} and Jan {Štourač} and Jiří {Damborský} and David {Bednář}",
  title="Fully Automated Ancestral Sequence Reconstruction using FireProtASR",
  journal="Current Protocols in Bioinformatics",
  year="2021",
  volume="1",
  number="2",
  pages="1--5",
  doi="10.1002/cpz1.30",
  issn="1934-3396",
  url="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.30"
}