Related papers: Protein domain connectivity and essentiality
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
The characterization of the "most connected" nodes in static or slowly evolving complex networks has helped in understanding and predicting the behavior of social, biological, and technological networked systems, including their robustness…
The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party…
Interactions between units in phyical, biological, technological, and social systems usually give rise to intrincate networks with non-trivial structure, which critically affects the dynamics and properties of the system. The focus of most…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
There has been tremendous development of linear controllability of complex networks. Real-world systems are fundamentally nonlinear. Is linear controllability relevant to nonlinear dynamical networks? We identify a common trait underlying…
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…
The identification of essential proteins can help in understanding the minimum requirements for cell survival and development. Network-based centrality approaches are commonly used to identify essential proteins from protein-protein…
The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and the limited overlap between the two disciplines have thus far…
Motivation: Protein-protein interactions (PPIs) are usually modelled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
It has been observed that the topology of the native state is an important determinant of protein folding kinetics and there is a significant correlation between folding rate and relative contact order (RCO) in two-state small single-domain…
Networks have been used to model many real-world phenomena to better understand the phenomena and to guide experiments in order to predict their behavior. Since incorrect models lead to incorrect predictions, it is vital to have a correct…
Self-avoiding random walks were performed on protein residue networks. Compared with protein residue networks with randomized links, the probability of a walk being successful is lower and the length of successful walks shorter in…
Data describing the three-dimensional structure of physical networks is increasingly available, leading to a surge of interest in network science to explore the relationship between the shape and connectivity of physical networks. We…
One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed…
One key task in virtual screening is to accurately predict the binding affinity ($\triangle$$G$) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the…
Networks in the real world do not exist as isolated entities, but they are often part of more complicated structures composed of many interconnected network layers. Recent studies have shown that such mutual dependence makes real networked…
We consider networks with two types of nodes. The v-nodes, called centers, are hyperconnected and interact one to another via many u-nodes, called satellites. This centralized architecture, widespread in gene networks, realize a bow-tie…