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

Taushif Khan; Shailesh Kumar Panday; Indira Ghosh

doi:10.1186/s12859-018-2171-9

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

BMC Bioinformatics. 2018 May 4;19(1):167. doi: 10.1186/s12859-018-2171-9.

Authors

Taushif Khan¹, Shailesh Kumar Panday², Indira Ghosh²

Affiliations

¹ School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India. taushifkhan@gmail.com.
² School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.

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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Neural Networks, Computer*
Proteins / chemistry*

Substances

Proteins