AlphaFold2 Update and Perspectives

Abstract

Access to the three-dimensional (3D) structural information of macromolecules is of major interest in both fundamental and applied research. Obtaining this experimental data can be complex, time consuming, and costly. Therefore, in silico computational approaches are an alternative of interest, and sometimes present a unique option. In this context, the Protein Structure Prediction method AlphaFold2 represented a revolutionary advance in structural bioinformatics. Named method of the year in 2021, and widely distributed by DeepMind and EBI, it was thought at this time that protein-folding issues had been resolved. However, the reality is slightly more complex. Due to a lack of input experimental data, related to crystallographic challenges, some targets have remained highly challenging or not feasible. This perspective exercise, dedicated to a non-expert audience, discusses and correctly places AlphaFold2 methodology in its context and, above all, highlights its use, limitations, and opportunities. After a review of the interest in the 3D structure and of the previous methods used in the field, AF2 is brought into its historical context. Its spatial interests are detailed before presenting precise quantifications showing some limitations of this approach and finishing with the perspectives in the field.

Keywords

• molecular modelling
• protein sequences
• protein structures
• comparative modelling
• threading
• de novo