Eleni Panagiotou

Entanglement-based continuum conformational landscape of proteins

The paper introduces mathematical topology metrics to quantify protein structure entanglement and represents the proteome in a continuous 3D space, showing structural and functional correlations.

Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants

The paper uses entanglement measures from knot theory to analyze sequence and structural features of intrinsically disordered proteins and identifies functionally enriched regions in entanglement space.

The local topological free energy of the SARS-CoV-2 Spike protein

This paper calculates the local topological free energy of the SARS-CoV-2 Spike protein and links it to protein rearrangement and mutation effects.

The protein folding rate and the geometry and topology of the native state

The paper analyzes protein folding rates and shows they depend on both local geometry and topology of the native state, using knot theory to quantify topological features.

The topological free energy of proteins

The paper introduces a local topological free energy metric for proteins and shows it correlates with folding rates in 2-state single domain proteins.