SCOP / CATH or other structural feature enrichment analyses using proteins

Question

[Khader Shameer]

I am working on a proteomics dataset. I am looking for a tool or service to enrichment analyses using protein IDs as query and provide the class, family, superfamily or fold terms (or class, architecture, topology or hierarchy) as output of enrichment analytics

DAVID had an implementation using SCOP in the past, but after the recent update - they removed it. It was a very useful utility for our drug discovery and nanobioinformatics projects.

I am wondering if there is any other tools/service or package out there to do such protein structure-based annotation and enrichment analyses. Thanks!

[natasha.sernova]

You probably need something similar to PFam.

https://nar.oxfordjournals.org/content/44/D1/D279.long

The Pfam protein families database: towards a more sustainable future

There are a few new tools:

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003929

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations

http://csbg.cnb.csic.es/PB/

Practical Protein Bioinformatics, 2015

Some special proteins:

https://www.bioconductor.org/packages/devel/bioc/vignettes/ABAEnrichment/inst/doc/ABAEnrichment.html

ABAEnrichment: gene expression enrichment in human brain regions

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-254

PhenoFam-gene set enrichment analysis through protein structural information, 2010

and these posts:

Tool For Evolutionary Conservation Of Protein Folds

PSEA- protein set enrichment analsyis

How To Measure Gene Enrichement (Go, Kegg) Using R And Ensembl Ids ?

Missing Pdb Enteries In Scop And Cath

This is around now-a-days.

[Khader Shameer]

Pfam is what am using at the moment. But, Pfam is at the level of domains which is equivalent to SCOP domains/family. I am more in interested in the higher order classification like superfamily and folds. dcGOR is interesting but won't do an enrichment over proteins, once I have set of SCOP data elements, it does some mapping to GO, etc. Other links/posts are not relevant.

[Sej Modha]

Have you looked at InterProScan?

[Jean-Karim Heriche]

Have you looked at PFAM clans ? My understanding is that they roughly correspond to SCOP superfamilies.