The ProLego server application explores the component aspect of Protein Structure space. ProLego, investigates the modularity in protein structures using in-house developed "contact string" (A Topological representation)
Protein building blocks as an analogy to "Lego® bricks"Legos are small and simple components used to build various shapes. From our extensive analysis of available protein structure space, we have shown that protein structures are composed of smaller building blocks or "modules". These modules can be used as "lego-blocks" for investigation and(or) designing new proteins.
Why "Pro-Lego"?With Pro-Lego, we provide an application that generates the protein topology string (or contact string) and a platform to vizualise in simple topological graphs. Encompassing the analysis on non-redundant protein structure data sets, we also list the variation in topological space (ProLegoDB).
See "Khan, T., Panday, S.K. and Ghosh, I., 2018. ProLego: tool for extracting and visualizing topological modules in protein structures. BMC bioinformatics, 19(1), p.167." for more details.
Contact String the Topology representation : Given a protein structure, ProLego enumerates constituent secondary structures and their arrangements. This is represented as a unique 1D string.
Generate topology visualization:
Topology Classifier: Comparing the obtained “contact string” with studied datasets, ProLego assigns frequency of occurrence status (prevalent/non-prevalent) for the corresponding topology. If the topology is not available in the dataset it should be able to update database on the fly.
Module Analysis: Given a contact String ProLego server can extract all the possible modules and searches similar proteins in the database.
Contact Map: Plots secondary structure contact map given a protein structure
