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arXiv · 2309.09955

The Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design

Chase Armer·Hassan Kane·Dana Cortade·Dave Estell·Adil Yusuf·Radhakrishna Sanka·Henning Redestig·TJ Brunette·Pete Kelly·Erika DeBenedictis
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Abstract

The grand challenge of protein engineering is the development of computational models that can characterize and generate protein sequences for any arbitrary function. However, progress today is limited by lack of 1) benchmarks with which to compare computational techniques, 2) large datasets of protein function, and 3) democratized access to experimental protein characterization. Here, we introduce the Protein Engineering Tournament, a fully-remote, biennial competition for the development and benchmarking of computational methods in protein engineering. The tournament consists of two rounds: a first in silico round, where participants use computational models to predict biophysical properties for a set of protein sequences, and a second in vitro round, where participants are challenged to design new protein sequences, which are experimentally measured with open-source, automated methods to determine a winner. At the Tournament's conclusion, the experimental protocols and all collected data will be open-sourced for continued benchmarking and advancement of computational models. We hope the Protein Engineering Tournament will provide a transparent platform with which to evaluate progress in this field and mobilize the scientific community to conquer the grand challenge of computational protein engineering.

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Chase Armer, Hassan Kane, Dana Cortade, Dave Estell, Adil Yusuf, Radhakrishna Sanka, Henning Redestig, TJ Brunette, Pete Kelly, Erika DeBenedictis. 2023-09-18. The Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design. https://doi.org/10.1002/prot.70008

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