Related papers: Protein domain connectivity and essentiality
Many complex natural and physical systems exhibit patterns of interconnection that conform, approximately, to a network structure referred to as scale-free. Preferential attachment is one of many algorithms that have been introduced to…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could…
Genetic interactions have been widely used to define functional relationships between proteins and pathways. In this study, we demonstrated that yeast synthetic lethal genetic interactions can be explained by the genetic interactions…
Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs…
The concept of nestedness, in particular for ecological and economical networks, has been introduced as a structural characteristic of real interacting systems. We suggest that the nestedness is in fact another way to express a mesoscale…
The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices…
Hub importance scores in multilayer networks persist more strongly between functionally similar layers than dissimilar ones. We call this the Functional Proximity Law and test it across 23 pre-registered experiments: 13 canonical domains…
Hierarchy and centrality are two popular notions used to characterize the importance of entities in complex systems. Indeed, many complex systems exhibit a natural hierarchical structure, and centrality is a fundamental characteristic…
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Relevance and importance are the main factors when humans build network connections. We propose an evolutionary network model based on preferential attachment(PA) considering these factors. We analyze and compute several important features…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
Active centres and hot spots of proteins have a paramount importance in enzyme action, protein complex formation and drug design. Recently a number of publications successfully applied the analysis of residue networks to predict active…
Though online social network research has exploded during the past years, not much thought has been given to the exploration of the nature of social links. Online interactions have been interpreted as indicative of one social process or…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
We study numerically domain growth and interface fluctuations in one- and two-dimensional lattice systems composed of four species that interact in a cyclic way. Particle mobility is implemented through exchanges of particles located on…