The residue interaction network (RIN) is widely used to analyze the topology and the dynamics of complex systems. RIN represents a three-dimensional protein structure as a set of nodes (residues) with their connections (edges). Calculated topological parameters from RIN correlate with various aspects of protein structure and function. Network analysis has been successfully used in different fields. In biology, this method is widely used for analysis of networks of gene regulation, protein–protein interaction, metabolites flow, prediction of drug side effects, etc.
Degree: A degree of a node is a number of edges in a network that connect node with its neighbors.
Connectivity: A connectivity represents minimum number edges that need to be removed to make a disconnected graph.
Shortest path: A shortest path is a path in which the two nodes are connected by the smallest number of intermediate nodes.
Closeness: A closeness centrality of a node is the reciprocal of the average shortest path length.
Betweenness centrality: A betweenness centrality of a node is the number of times that a node is included in the shortest path between each pair of nodes, normalized by the total number of pairs.
|Project name||Residue interaction network service|
|Samples requirement||Our residue interaction network service requires you to provide specific requirements.|
|Timeline||Decide according to your needs.|
|Deliverables||We provide you with raw data and modeling results.|
The identification of ligand binding sites for protein and functionally important residues is a crucial first step in drug design. Several topological parameters of RIN can be used to predict ligand binding sites. Several studies have shown that the tightness and intermediate value of the residues are related to the ligand binding site residues, so they can be used to predict the binding site.
Protein–protein interactions (PPIs) are crucial for many biological processes and functions; inhibition of PPIs with small molecules is a perspective way in drug design. RIN method can be used for analysis of protein–protein interfaces, prediction of hotspots, and selection of protein poses in the protein–protein docking.
Using allosteric sites for drug design, it is required to predict allosteric sites, residues involved in signal transduction pathways to the active sites. RIN is an accurate and efficient method for prediction such pathways.
RIN may be used for analysis and prediction of effects of amino acid mutation on protein properties, which may be useful for protein design, investigations of disease-associated single nucleotide polymorphisms, or mechanism of the drug resistance.
CD ComputaBio provides corresponding network service. Our residue interaction services have proven to be very useful for understanding the biochemical basis of physiological events at different stages of drug development (even in different fields such as materials science). CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals. If you have a need for network analysis services, please feel free to contact us.