Prediction of structural variation

Abstract

Proteins are dynamic molecules that transition between conformational states to perform their functions, and characterizing the protein ensemble is important for understanding biology and therapeutic applications. While recent breakthroughs in machine learning have enabled the prediction of high-quality static models of individual proteins, generating reliable estimates of their conformational ensembles remains a challenge. Several recent methods have tried to utilize the evolutionary and structural features captured by effective sequence-to-structure models to enhance conformational diversity in generated models. Most of these approaches involve adapting existing inference pipelines, such as AlphaFold 2, combined with sampling techniques to induce the generation of diverse conformational states. Here, we describe the general problem of predicting structural variations in protein systems, explain the methods designed to address this challenge, explore why they are effective, discuss their limitations, and suggest potential future directions.