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In Silico-Directed Evolution Using CADEE.

Beat Anton Amrein1, Ashish Runthala2, Shina Caroline Lynn Kamerlin3

  • 1Associate Scientist, Tecan Schweiz AG, Männedorf, Switzerland. beat.amrein@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|October 10, 2018
PubMed
Summary

Computer-aided directed evolution (CADEE) offers new ways to evolve enzymes computationally. This work details the CADEE workflow, enabling users to perform enzyme evolution simulations for any target system.

Keywords:
Computational enzyme designComputational enzymologyDirected evolutionEmpirical valence bondEnzyme design

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Area of Science:

  • Computational biology
  • Enzyme engineering
  • Bioinformatics

Background:

  • Directed evolution is crucial for enzyme engineering.
  • In silico methods are gaining traction for enzyme evolution.
  • A novel computational toolkit, CADEE, was developed for computer-aided directed evolution.

Purpose of the Study:

  • To provide a detailed description of the CADEE workflow.
  • To enable users to apply CADEE to their own enzyme systems.
  • To illustrate the practical application of computational enzyme engineering.

Main Methods:

  • Detailed explanation of the Computer-Aided Directed Evolution (CADEE) workflow.
  • Inclusion of code input/output snippets for practical guidance.
  • Application of CADEE to triosephosphate isomerase as a pedagogical example.

Main Results:

  • A comprehensive guide to the CADEE simulation process.
  • Demonstration of CADEE's utility in enzyme evolution.
  • Facilitation of user-independent execution of CADEE simulations.

Conclusions:

  • The detailed CADEE workflow empowers researchers to conduct in silico enzyme evolution.
  • CADEE provides a flexible platform for computational enzyme engineering.
  • This work lowers the barrier for applying advanced computational tools in enzyme discovery and optimization.