Related papers: Information and Protein Interfaces
We study mixing patterns in networks, meaning the propensity for nodes of different kinds to connect to one another. The phenomenon of assortative mixing, whereby nodes prefer to connect to others that are similar to themselves, has been…
We consider two (2D) and three (3D) dimensional granular systems exposed to compression, and ask what is the influence of the number of physical dimensions on the properties of the interaction networks that spontaneously form as these…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large…
Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for…
Probabilistic representation spaces convey information about a dataset and are shaped by factors such as the training data, network architecture, and loss function. Comparing the information content of such spaces is crucial for…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
In a comment on our manuscript "Strong selection significantly increases epistatic interactions in the long-term evolution of a protein", Dr. Crona challenges our assertion that shared entropy (that is, information) between two residues…
Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
In statistical physics entropy is usually introduced as a global quantity which expresses the amount of information that would be needed to specify the microscopic configuration of a system. However, for lattice models with infinitely many…
Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two…
An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…