DynaSIN: Integration of Protein Motions with Molecular Networks


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Gerstein Lab


The integration of macromolecular structure data into protein-protein interaction networks promises to offer novel insights into biological network behavior and organization. The Dynamic Structure Interaction Network (DynaSIN) constitutes a resource for studying such networks in the context of protein conformational changes. Constructed by parsing the PDB for alternate conformations of proteins, and mapping these conformations onto the protein interaction network, DynaSIN is available as readily downloadable resource files. Related efforts have enabled the classification of network proteins on the basis of their number of distinct binding interfaces, as well as the classification of interactions as transient and permanent, depending on whether a given interface is used by one or multiple partners. Using DynaSIN, we have identified disparities between different classes of proteins and interactions, in light of conformational changes.

Nitin Bhardwaj, Alexej Abyzov, Declan Clarke, Chong Shou, and Mark B. Gerstein (2011) Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 20:1745-1754.

nbhardwaj@gmail.com or Mark.Gerstein@yale.edu

Copyright (c) Gerstein Lab 2011