Part I: Steps followed for naming a superfamily
- Look through representative domains as: ‘domain only’ to understand common secondary structures; as ‘domain in chain’ to observe the location of the domain in the chain; as ‘domain in PDB’ to understand the domain’s function and location in the protein.
- Check through FunFams/SwissProt/Keywords and refer to the most abundant name when naming.
- Check through enzymes (EC number if available), GO terms and species to get a rough idea of domain function.
- Refer to Pfam and InterPro entries for general idea of protein domain function and/or structure.
- Check through papers associated with PDB entry for better understanding of protein and protein domain structure and/or function .
- In ‘Description section’, provide an overview of structure and function. In larger superfamilies, you may have to refer to specific PDB IDs.
- Check references are correct: [InterPro:] [Pfam:] [PMID:] [DOI:]
- Check other names in the database, either to avoid duplicate names or to identify potential cross-hits
- Check names of other domains in the same chain to keep the name similar.
Part II: General observations and tips
- Check other names in CATH to not make duplicates (i.e. make sure the assigned name is unique)
- Make superfamily names consistent with other domains of same protein
- Start with smaller families until you get the hang of it
- For larger superfamily- it is a good idea to check FunFam
- When looking at a protein on InterPro, see if there are other domains that don’t have a name yet on the same protein - it will be easy to name that one
- Work in groups for larger superfamilies
- Choose superfamily entries with FunFams, Pfams, or InterPro associated
- Make description without sourcing references
- Make description without actually really understanding it
- Spend 3 hours on a very small superfamily
- Look at every single PDB for big superfamilies
- For smaller representative domains, don’t put too much confidence in InterPro/Pfam - it may be better to look at PDB paper for the specific domain
- Assume it is the exact same domain if it has good mapping to Pfam
- Choose a superfamily entry with no annotation or too many annotation
(Last updated in September 2023, Written by summer interns since 2020-2023 (Barbara, Oliver, Natalie, Charling, Ruiqi, Lorna, Katie, Charlotte, Hazuki) and CATH curators (Vaishali Waman, Ian Sillitoe)