Synthical logo
Your space
From chemRxiv
Vanderbilt University

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation

Directed evolution facilitates enzyme engineering via iterative rounds of mutagenesis. Despite the wide applications of high-throughput screening, building “smart libraries” to effectively identify beneficial variants remains a major challenge in the community. Here, we developed a new computational directed evolution protocol based on EnzyHTP, a software we have previously reported to automate enzyme modeling. To enhance the throughput efficiency, we implemented an adaptive resource allocation strategy that dynamically allocates different types of computing resources (e.g., GPU/CPU) based on the specific need of an enzyme modeling sub-task in the workflow. We implemented the strategy as a Python library and tested the library using fluoroacetate dehalogenase as a model enzyme. The results show that comparing to fixed resource allocation where both CPU and GPU are on-call for use during the entire workflow, applying adaptive resource allocation can save 87% CPU hours and 14% GPU hours. Furthermore, we constructed a computational directed evolution protocol under the framework of adaptive resource allocation. The workflow was tested against two rounds of mutational screening in the directed evolution experiments of Kemp eliminase with a total of 184 mutants. Using folding stability and electrostatic stabilization energy as computational readout, we reproduced three out of the four experimentally-observed target variants. Enabled by the workflow, the entire computation task (i.e., 18.4 μs MD and 18,400 QM single point calculations) completes in three days of wall clock time using ~30 GPUs and ~1000 CPUs.
Published on June 20, 2023
Copy BibTeX
There is no AI-powered summary yet, because we do not have a budget to generate summaries for all articles.
1. Buy subscription
We will thank you for helping thousands of people to save their time at the top of the generated summary.
If you buy our subscription, you will be able to summarize multiple articles.
Pay $undefined
≈10 summaries
Pay $undefined
≈60 summaries
2. Share on socials
If this article gets to top-5 in trends, we'll summarize it for free.
Copy link