Exploring predictions of protein functional sites using FunFams in CATH-Gene3D

This training workflow introduces how to search (using query protein sequences) for functional site residues and predicted Functional Families (FunFams) using CATH-Gene3D.

It is designed to lead you through the process of finding sequence or structure information for your protein of interest e.g. sequence from UniProt and structure from PDBe, and using it as a search query in the CATH-Gene3D resource.

It will then help guide you through exploring and interpreting the predicted functional information to give you greater understanding of key protein features and sites - along with knowledge of how genetic variation may impact on the structure/function.

By following through the material you will learn:

1. How use a sequence for your protein of interest to search against the CATH protein family resource
2. How to identify structural domains in your protein and how to find out whether the identified domain family matches are reliable
3. How to look at the multiple-sequence alignment of your protein with your domain family match and find the positions that are highly conserved in the alignment and which are therefore likely to be functionally important.

Typical users are expected to be wet-lab biologists, or even bioinformaticians unfamiliar with this aspect of computational biology, who have identified a protein of interest from their research - and who wish to explore the function of the protein in a structural context.

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