Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids

TL;DR

Knoto-ID is a novel tool that analyzes the entanglement of open protein chains directly using knotoid theory, avoiding the need for curve closure and enabling detection of complex topological features.

Contribution

It introduces a new method for studying open protein chain entanglement with knotoids, improving detection of non-trivial folds beyond existing knot-based approaches.

Findings

Identifies topologically non-trivial protein folds missed by previous tools.

Analyzes both global and local topology of protein chains.

Provides a means to study open curves without closure artifacts.

Abstract

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds.