Protein structure and function data at PDBe-KB

Proteins are the workhorses of the cell, responsible for most biological functions. Though we can group related proteins through sequence similarity, it is the 3-dimensional structure of these proteins that determines the functions of these molecules of life. Therefore, knowledge of protein structure, and its relation to additional biological context, can help us create a more complete understanding of how a protein works.

PDBe-KB is an open, collaborative data resource, which aims to support the access and integration of structural biology data helping users to easily generate biological insights. The Aggregated Views of Proteins, provided through PDBe-KB, provide a unique way to display all the relevant structure and function data for a specific protein, in one place. This allows us to determine trends across these structures, including common binding and interaction sites, and identification of different conformations of the protein.

This webinar with Joseph Ellaway (Bioinformatician, EMBL-EBI) and Marcelo Querino (Bioinformatician, EMBL-EBI), recorded on 18 October 2023, provides an introduction to the PDBe-KB Aggregated Views of Proteins and how they can be used to access and interpret structure and function data.

Learning outcomes:

By the end of this video you will be able to:

• Navigate and utilise tools on PDBe-KB webpages to get an overview of available structural and functional information on your proteins of interest
• Visualise superposed protein chains clustered by structural similarity for any protein in PDB
• Download the relevant data for your protein of interest

The collaboration between Google DeepMind and PDBe has led to the creation of AlphaFold, a tool capable of predicting the three-dimensional structure of a protein based on its amino acid sequence. The following section will introduce the AlphaFold Database, presenting a repository of predicted protein structures along with methods for their assessment.