Mining databases for protein aggregation: a review

Abstract

Protein aggregation is an active area of research in recent decades, since it is the most common and troubling indication of protein instability. Understanding the mechanisms governing protein aggregation and amyloidogenesis is a key component to the aetiology and pathogenesis of many devastating disorders, including Alzheimer’s disease or type 2 diabetes. Protein aggregation data are currently found “scattered” in an increasing number of repositories, since advances in computational biology greatly influence this field of research. This review exploits the various resources of aggregation data and attempts to distinguish and analyze the biological knowledge they contain, by introducing protein-based, fragment-based and disease-based repositories, related to aggregation. In order to gain a broad overview of the available repositories, a novel comprehensive network maps and visualizes the current association between aggregation databases and other important databases and/or tools and discusses the beneficial role of community annotation. The need for unification of aggregation databases in a common platform is also addressed.

Keywords:

• Protein aggregation
• amyloid
• amyloidosis
• amyloidogenesis
• database

Acknowledgements

The authors sincerely thank the Editor in Chief for properly handling this manuscript and both the Associate Editor and the anonymous reviewers for their very useful and constructive criticism, which helped to considerably improve the manuscript. We also thank the University of Athens for support.

Disclosure statement

The authors declare no conflict of interest

Additional information

Funding

This project was financially supported by the Greek State Scholarships Foundation, through the program “Research Projects for Excellence IKY/Siemens” (2015–2017).