RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins

Ahmed A Quadeer¹, David Morales-Jimenez², Matthew R McKay^1,3

¹Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.

|December 5, 2019

Summary

Robust Co-evolutionary Analysis (RoCA) predicts protein co-evolutionary sectors linked to function. A new package, RocaSec, offers a user-friendly GUI for easy application to protein sequence data.

Area of Science:

Computational Biology
Bioinformatics
Protein Science

Background:

Mutational correlation patterns in protein sequences reveal co-evolutionary sectors.
These sectors are linked to protein function and structure.
Robust Co-evolutionary Analysis (RoCA) is a statistical method for predicting these sectors, validated on viral proteins.

Purpose of the Study:

To introduce RocaSec, a standalone, cross-platform software package with a graphical user interface (GUI).
To simplify and broaden the application of RoCA for inferring protein co-evolutionary sectors.
To enable the analysis of statistical associations between inferred sectors and known biochemical domains.

Main Methods:

Development of a user-friendly GUI for the RoCA method.
The software requires only a multiple sequence alignment of a protein as input.
Optional input of protein biochemical domain information to correlate with inferred sectors.

Main Results:

RocaSec provides a streamlined approach to infer co-evolutionary sectors from protein sequence data.
The software demonstrates ease of use and cross-platform compatibility.
It facilitates the statistical association of predicted sectors with known protein biochemical domains.

Conclusions:

RocaSec enhances the accessibility and application of co-evolutionary analysis in protein research.
The tool aids in understanding protein structure-function relationships by linking sequence-derived sectors to biochemical domains.
Widespread adoption of RocaSec is expected to advance the study of protein evolution and function.

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RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins

Area of Science:

Background:

Purpose of the Study:

Main Methods:

Main Results:

Conclusions:

Related Concept Videos

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