T. Skrbic

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

The paper compares simulations of polymer chains and experimental data on protein structures to analyze their geometries and reconcile differences through symmetry considerations.

Amino acid characteristics in protein native state structures

The paper analyzes side chain protrusion statistics in protein structures to understand amino acid behavior in native states.

III. Geometrical framework for thinking about globular proteins: turns in proteins

The paper introduces a geometrical framework to understand protein turns by defining them as isolated local poking interactions, identifying their structural classes and amino acid preferences.

II. Geometrical framework for thinking about globular proteins: the power of poking

The paper benchmarks a geometrical model of protein structure using structural data and simulations, showing that symmetry and geometry can explain protein complexity through poking interactions.

A geometrical framework for thinking about proteins

The paper introduces a geometrical model of proteins based on symmetry and geometry, showing it aligns with experimental data and explains protein structure and function.

Marginally compact phase and ordered ground states in a model polymer with side spheres

This study investigates the phase behavior of a polymer model with side spheres, revealing a marginally compact phase with ordered structures and first-order transitions.

Spontaneous dimensional reduction and novel ground state degeneracy in a simple chain model

The paper studies a homopolymer model of a linear chain molecule, finding a first-order phase transition, ground state degeneracy, spontaneous dimensional reduction, and a two-layer structure composed of helices and strands connected by loops.

Building blocks of protein structures - Physics meets Biology

This paper derives the geometry of protein building blocks using physics and mathematics without sequence or chemistry, showing a perfect fit with quantum chemistry and implications for artificial life.