Detail publikace

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

HON, J. BORKO, S. ŠTOURAČ, J. PROKOP, Z. BEDNÁŘ, D. ZENDULKA, J. MARTÍNEK, T. DAMBORSKÝ, J.

Originální název

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible source of biocatalysts. Despite genomic databases growing exponentially, classical biochemical characterization techniques are time-demanding, cost-ineffective and low-throughput. Therefore, computational methods are being developed to explore the unmapped sequence space efficiently. Selection of putative enzymes for biochemical characterization based on rational and robust analysis of all available sequences remains an unsolved problem. To address this challenge, we have developed EnzymeMiner - a web server for automated screening and annotation of diverse family members that enables selection of hits for wet-lab experiments. EnzymeMiner prioritizes sequences that are more likely to preserve the catalytic activity and are heterologously expressible in a soluble form in Escherichia coli. The solubility prediction employs the in-house SoluProt predictor developed using machine learning. EnzymeMiner reduces the time devoted to data gathering, multi-step analysis, sequence prioritization and selection from days to hours. The successful use case for the haloalkane dehalogenase family is described in a comprehensive tutorial available on the EnzymeMiner web page. EnzymeMiner is a universal tool applicable to any enzyme family that provides an interactive and easy-to-use web interface freely available at https://loschmidt.chemi.muni.cz/enzymeminer/.

Klíčová slova

computational characterization, enzyme mining, enzyme diversity, novel biocatalysts

Autoři

HON, J.; BORKO, S.; ŠTOURAČ, J.; PROKOP, Z.; BEDNÁŘ, D.; ZENDULKA, J.; MARTÍNEK, T.; DAMBORSKÝ, J.

Vydáno

2. 6. 2020

ISSN

1362-4962

Periodikum

Nucleic Acids Research

Ročník

48

Číslo

1

Stát

Spojené království Velké Británie a Severního Irska

Strany od

104

Strany do

109

Strany počet

6

URL

https://www.fit.vut.cz/research/publication/12197/

BibTex

@article{BUT168156,
  author="Jiří {Hon} and Simeon {Borko} and Jan {Štourač} and Zbyněk {Prokop} and David {Bednář} and Jaroslav {Zendulka} and Tomáš {Martínek} and Jiří {Damborský}",
  title="EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities",
  journal="Nucleic Acids Research",
  year="2020",
  volume="48",
  number="1",
  pages="104--109",
  doi="10.1093/nar/gkaa372",
  issn="1362-4962",
  url="https://www.fit.vut.cz/research/publication/12197/"
}

Dokumenty

EnzymeMiner.pdf