Residue Interaction Network Service

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.

Common characteristics

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.

Residue Interaction Network Service 1

Overall Solution

  • We can provide complex analysis of proteins and their complexes by using RINs analysis.
  • We can provide you with estimation about their interdependence and to predict the different properties and functions of individual residues and entire proteins.
  • We can analyze the chemical and physical properties of the base and the energy of their interaction through the construction of RIN.
  • We can study the structure and function of proteins through RINs, which can be applied to drug design in many ways.

Our PPI network service

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.
Price Inquiry

Features

  • The development of inhibitors of protein–protein interactions is a perspective way in drug design, and RIN showed their applicability for this purpose.
  • The analysis of networks may help to select correct poses in protein–protein docking that is important for the selection of inhibitor binding sites.
  • RINs are convenient for finding allosteric sites, investigation of mechanism of intraprotein signal transmission.

Residue Interaction Network Service 2

Applications for PPI network service

Residue Interaction Network Service 3

  • Ligand Binding Site

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.

Residue Interaction Network Service 4

  • Protein–Protein Interactions

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.

  • Allosteric Regulation

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.

  • Analyses of Mutations

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.

We provide a variety of modeling services, but not limited to:

* For Research Use Only.

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