Knoto-ID

Knoto-ID analyzes entanglement in open protein chains using the mathematical framework of knotoids to characterize backbone topology without closing chains into loops.

Key Features:

• Knotoid Concept: Applies knotoids, an extension of classical knot theory for open curves, to evaluate entanglement without altering the protein backbone by loop closure.
• Global and Local Topology Analysis: Performs global topology assessment of entire protein chains and local topology analysis via exhaustive examination of all subchains and identification of knotted cores.
• Detection of Non-Trivial Folds: Detects topologically non-trivial protein folds that can be missed by conventional knot-detection methods.
• Visualization Tools: Provides R scripts to generate projection maps, fingerprint matrices, and disk matrices for representation of topological data.
• Implementation: Implemented in C++ and distributed under the GNU General Public License (GPL) version 2 or later.

Scientific Applications:

• Protein topology characterization: Characterizes backbone entanglement to inform studies of protein folding, stability, and structure-function relationships.
• Discovery of non-trivial folds: Identifies folds beyond classical knots, extending the scope of protein topology studies.
• Local folding motif analysis: Maps local knotted regions and subchain entanglement to analyze local folding motifs and knotted cores.

Methodology:

Analyzes protein backbones as open curves using the knotoid mathematical framework without closing chains into loops and systematically examines subchains to identify knotted cores and characterize topology.