Related papers: Simplicial edge representation of protein structur…
Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
Particle-based shape modeling (PSM) is a family of approaches that automatically quantifies shape variability across anatomical cohorts by positioning particles (pseudo landmarks) on shape surfaces in a consistent configuration. Recent…
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Predicting the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Graph representations of solid state materials that encode only interatomic distance lack geometrical resolution, resulting in degenerate representations that may map distinct structures to equivalent graphs. Here we propose a hypergraph…
Fractal structure of shortest paths depends strongly on interresidue interaction cutoff distance. The dimensionality of shortest paths is calculated as a function of interaction cutoff distance. Shortest paths are self similar with a…