PDBeFold: Searching for structural homologues of a protein

Gary Battle [1] Proteins Structures Beginner 1 hour PDBeFold can be used to identify structural homologues in the PDB. PDBe's Secondary Structure Matching service (SSM) allows you to interactively compare, align and superimpose protein structures in 3D. This course will show you how to use PDBeFold and what you can do with it. An undergraduate degree in a life science subject would be an advantage. You may wish to look at the PDBe quick tour [2] and Biomacromolecular structures [3] course as an introduction to this tutorial. Evaluate what PDBeFold is and what it can do Be able to launch PDBeFold and search for 3D structures that are similar to your protein of interest Interpret structural similarity of your results based on Q-scores Be able to view and analyse structures from your returned results What is PDBeFold? PDBeFold [4] is an interactive service that allows you to identify structures that are similar to that of your reference protein. It is a very powerful structure alignment tool which can perform both pairwise and multiple three-dimensional alignment. In addition, PDBeFold gives you various options to sort the results of your structural alignment query.