ActifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions.

ABSTRACT:

Summary

One of the main advantages of deep learning models of protein structure, such as Alphafold2, is their ability to accurately estimate the confidence of a generated structural model, which allows us to focus on highly confident predictions. The ipTM score provides a confidence estimate of interchain contacts in protein-protein interactions. However, interactions, in particular motif-mediated interactions, often also contain regions that remain flexible upon binding. These noninteracting flanking regions are assigned low confidence values and will affect ipTM, as it considers all interchain residue-residue pairs, and two models of the same motif-domain interaction, but differing in the length of their flanking regions, would be assigned very different values. Here, we propose

SUBMITTER: Varga JK 

PROVIDER: S-EPMC11925850 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature