PiQSi: Protein Quaternary Structure Investigation

Abstract

PiQSi facilitates the manual investigation of the quaternary structure of protein complexes in the Protein Data Bank (PDB). Users can browse and obtain an overview of the quaternary structure information of a given protein together with its evolutionary relatives, which helps in the determination of the biological quaternary state. I have used this framework to annotate over 10,000 structures from the PDB Biological Unit and corrected the quaternary state of approximately 15% of them. A benchmark shows that the annotations are of high quality and stresses the need for manual curation, in particular for ambiguous cases such as proteins in equilibrium between two quaternary states. The approximately 10,000 annotations already in the database can be used to improve the accuracy of analyses on protein structure or to benchmark methods that predict protein quaternary structure. In addition, PiQSi incorporates a community-based curation system, which I hope will allow us to reach an accurate and complete description of the biological quaternary state of proteins in PDB. PiQSi is accessible at http://www.PiQSi.org/.