Protein Structural Network

The structure of a protein can be analyzed based on the network formalism using tools such as Protein Structural Networks (PSN). A node-edge representation of a protein structure, modeling the residues as nodes and edges between nodes that interact can be termed as a PSN. There are interesting methods to construct networks from protein structure. Most common methods involve the spatial proximity between resides to identify interactions as edges of the PSN. Here, I have a compilation of network tools that I find from my personal research that can be useful for studying protein structures.

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ANCA: A Web Server for Amino Acid Networks Construction and Analysis
paper

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ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
paper, link

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RIP-MD: a tool to study residue interaction networks in protein molecular dynamics
paper 

Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. http://www.dlab.cl/ripmd

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NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

RINs have also been adopted for the prediction of the effect of single point mutations in protein stability (Giollo et al., 2014);

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