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

Taushif Khan,Indira Ghosh,Shailesh Kumar Panday

doi:10.1186/s12859-018-2171-9

Abstract

BackgroundIn 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.ResultWe 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.ConclusionProLego, provides an alternative but comprehensive way to scan and visualize protein topology along with an extensive database of protein topology.

Highlights

In protein design, correct use of topology is among the initial and most critical feature
Representing protein topology as a graph of secondary structure, ProLego provides visualization focusing on different representation (Fig. 1a)
ProLegoDB is an extensive database of protein topology generated by analysis of representative datasets (Additional file 1 section 1.7)

Summary

Introduction

Correct use of topology is among the initial and most critical feature. 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. Topology based approach has been recently exploited to examine the structure space of proteins and provide insights into fold designing and evolution [4,5,6,7]. Topology has been used extensively to address the nature of folding profile by both experimental and computational approaches [8]. Rockline et al [9], recently reported improvements in protein designing with extensive use of high-throughput topology scanning in case of 4 mini-proteins. The use of topology in the context of protein designing, folding and stability studies has been widely used

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