CCfrag: scanning folding potential of coiled-coil fragments with AlphaFold.

ABSTRACT:

Motivation

Coiled coils are a widespread structural motif consisting of multiple α-helices that wind around a central axis to bury their hydrophobic core. While AlphaFold has emerged as an effective coiled-coil modeling tool, capable of accurately predicting changes in periodicity and core geometry along coiled-coil stalks, it is not without limitations, such as the generation of spuriously bent models and the inability to effectively model globally non-canonical-coiled coils. To overcome these limitations, we investigated whether dividing full-length sequences into fragments would result in better models.

Results

We developed CCfrag to leverage AlphaFold for the piece-wise modeling of coiled coils. The user can create a specification, defined by window size, length of overl

SUBMITTER: Martinez-Goikoetxea M 

PROVIDER: S-EPMC11676326 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature