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. -- ANCA: A Web Server for Amino Acid Networks Construction and Analysis paper -- ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism paper , link -- 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 t...