ProLego: tool for extracting and visualizing topological modules in protein structures

Abstract

Abstract Background In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intuitive and efficient way to scan the protein topology space. Result We have implemented in-house developed “topological representation” in an automated-pipeline to extract protein topology from given protein structure. Using the topology string, ProLego, compares topology against a non-redundant extensive topology database (ProLegoDB) as well as extracts constituent topological modules. The platform offers interactive topology visualization graphs. Conclusion ProLego, provides an alternative but comprehensive way to scan and visualize protein topology along with an extensive database of protein topology. ProLego can be found at http://www.proteinlego.com

Keywords

• Protein topology
• Topology comparisons.
• Protein Graph.
• Visualization.
• Server application.