SecStrAnnotator:OneToMany: Difference between revisions
Created page with "Under construction... <br style="clear:both" /> ---- Back to the main page" |
No edit summary |
||
| Line 1: | Line 1: | ||
This page describes the procedure for annotating SSEs in a whole protein family. | |||
A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins). | |||
==Dependencies== | |||
Python3 | |||
==Preparing structural data== | |||
A list of PDB structures corresponding to a protein family can be obtained from [http://www.ebi.ac.uk/pdbe/pdbe-rest-api PDBe REST API] using <code>domains_from_pdbeapi.py</code>. The protein family can be identified by a CATH code, such as 1.10.630.10 ([http://cathdb.info/ CATH]), or a Pfam accession, such as PF00067 ([https://pfam.xfam.org/ Pfam]): | |||
python3 domains_from_pdbeapi.py 1.10.630.10 > family_from_cath.json | |||
or | |||
python3 domains_from_pdbeapi.py PF00067 > family_from_pfam.json | |||
The main stages of the procedure are: | |||
* preparing the structural data for the family | |||
* selecting a template domain from the family and obtaining its annotation | |||
* running the annotation algorithm (SecStrAnnotator) on each member of the family | |||
Revision as of 00:40, 1 May 2018
This page describes the procedure for annotating SSEs in a whole protein family.
A protein family is understood as a set of structurally similar protein domains. A protein domain can be either a whole protein chain or only a part of it (in multidomain proteins).
Dependencies
Python3
Preparing structural data
A list of PDB structures corresponding to a protein family can be obtained from PDBe REST API using domains_from_pdbeapi.py. The protein family can be identified by a CATH code, such as 1.10.630.10 (CATH), or a Pfam accession, such as PF00067 (Pfam):
python3 domains_from_pdbeapi.py 1.10.630.10 > family_from_cath.json
or
python3 domains_from_pdbeapi.py PF00067 > family_from_pfam.json
The main stages of the procedure are:
- preparing the structural data for the family
- selecting a template domain from the family and obtaining its annotation
- running the annotation algorithm (SecStrAnnotator) on each member of the family