EnzymeMiner: Automated Mining of Soluble Enzymes with Diverse Structures, Catalytic Properties and Stabilities

Authors

Hon, J., Borko, S., Stourac, J., Prokop, Z., Zendulka, J., Bednar, D., Martinek, T., Damborsky, J.

Source

NUCLEIC ACIDS RESEARCH 48: W104–W109 (2020)

Abstract

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/.

Full text

Citation

Hon, J., Borko, S., Stourac, J., Prokop, Z., Zendulka, J., Bednar, D., Martinek, T., Damborsky, J., 2020: EnzymeMiner: Automated Mining of Soluble Enzymes with Diverse Structures, Catalytic Properties and Stabilities. Nucleic Acids Research 48: W104–W109.

5th Hands-on Computational Enzyme Design Workshop
Jiri to Present at Biocatalysis Gordon Research Conference 2024
Interview with Martin – I Came Into My Own in the Microworld
Jiri and Pavel at Symposium: Biochemical Machine Learning
Lukas at International Science and Engineering Fair in Dallas
Jiri to Present at Elixir 3D Bio AGM
Press Release: We Are Closer to Treatment of Alzheimer’s Disease