相关论文: Modeling Protein Contact Networks
Numerous real-world systems can be naturally modeled as multilayer networks, enabling an efficient way to characterize those complex systems. Much evidence in the context of system biology indicated that the collections between different…
Protein representation learning is a challenging task that aims to capture the structure and function of proteins from their amino acid sequences. Previous methods largely ignored the fact that not all amino acids are equally important for…
In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological…
We propose a network model with a fixed number of nodes and links with a dynamics which favors links between nodes differing in connectivity. Parameter regimes where the degree distributions follow power-laws, P(k) ~ k^-gamma, high…
Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Clustering, assortativity, and communities are key features of complex networks. We probe dependencies between these attributes and find that ensembles with strong clustering display both high assortativity by degree and prominent community…
Networks are widely used in the biological, physical, and social sciences as a concise mathematical representation of the topology of systems of interacting components. Understanding the structure of these networks is one of the outstanding…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
A general relation for the dependence of nearest neighbor degree correlations on degree is derived. Dependence of local clustering on degree is shown to be the sole determining factor of assortative versus disassortative mixing in networks.…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
We examined protein residue networks (PRNs) from a local search perspective to understand why PRNs are highly clustered when having short paths is important for protein functionality. We found that by adopting a local search perspective,…
The budding yeast {\it Saccharomyces cerevisiae} is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual…
Networks describe a variety of interacting complex systems in social science, biology and information technology. Usually the nodes of real networks are identified not only by their connections but also by some other characteristics.…
A protein residue network (PRN) is a network of interacting amino acids within a protein. We describe characteristics of a sparser, highly central and more volatile sub-network of a PRN called the short-cut network (SCN), as a protein folds…
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
A single protein molecule is regarded as a contact network of amino-acid residues. Some studies have indicated that this network is a small world network (SWN), while other results have implied that this is a fractal network (FN). However,…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…