ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design

Abstract

Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins to address our most pressing challenges in climate, agriculture and healthcare. Despite an increase in machine learning-based protein modeling methods, assessing their effectiveness is problematic due to the use of distinct, often contrived, experimental datasets and variable performance across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym v1.0, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 40 high-performing models from various subfields (eg., mutation effects, inverse folding) into a unified benchmark. We open source the corresponding codebase, datasets, MSAs, structures, predictions and develop a user-friendly website that facilitates comparisons across all settings.