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--- data_curation:superfamily_naming_tutorial:index [2023/09/28 16:02] – vwaman
+++ data_curation:superfamily_naming_tutorial:index [2023/09/28 16:24] (current) – vwaman
@@ Line 1: / Line 1: @@
-[[data_curation:superfamily_naming_tutorial:index|Superfamily Naming exercise (Last updated in Sept 2023)]]
 === Superfamily Naming exercise (Last updated in Sept 2023) ===
-Useful websites:
+**Useful websites:**
 https://www.cathdb.info/
 http://sfam.cathdb.info/
 **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.
+  * 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 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.
+  * 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.
+  * 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 .
+  * 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.
+  * 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 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 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.
+  * Check names of other domains in the same chain to keep the name similar.
-Part II: General observations and tips
+**Part II: General observations and tips**
 Dos
-•	Check other names in CATH to not make duplicates (i.e. make sure the assigned name is unique)
+  * 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
+  * Make superfamily names consistent with other domains of same protein
-•	Start with smaller families until you get the hang of it
+  * Start with smaller families until you get the hang of it
-•	For larger superfamily- it is a good idea to check FunFam
+  * 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
+  * 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
+  * Work in groups for larger superfamilies
-•	Choose superfamily entries with FunFams, Pfams, or InterPro associated
+  * Choose superfamily entries with FunFams, Pfams, or InterPro associated
 Don’ts
-•	Make description without sourcing references
+  * Make description without sourcing references
-•	Make description without actually really understanding it
+  * Make description without actually really understanding it
-•	Spend 3 hours on a very small superfamily
+  * Spend 3 hours on a very small superfamily
-•	Look at every single PDB for big superfamilies
+  * 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
+  * 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
+  * 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
+  * 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)

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