SLiMSuite protocol cookbook

PPI SLiM prediction

These protocols make use of example data that can be found on OSF (DOI:10.17605/OSF.IO/8DTQ5).

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Protocol 1. Extract PPI partners

This can be done using the PINGU server and one of the PPI datasets on the server. For this example, yeast PPI data from the APID database will be used, along with the yeast PCNA orthologue POL30:

http://rest.slimsuite.unsw.edu.au/pingu&ppisource=Scer.apid-hq&hublist=POL30

Example JobID:19051500006

The uniprot output can then be used as input for SLiMSuite programs (see below). This output is also provided in the SLiMSuite data/ directory and OSF data as data/POL30.Scer.apid-hq.acc.

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Protocol 2: SLiM prediction with disorder masking

The output of one REST program can be fed directly into the input of another. In this case, the Spoke Uniprot accession numbers will be used as input for SLiMFinder:

http://rest.slimsuite.unsw.edu.au/slimfinder&uniprotid=jobid:19051500006:uniprot&dismask=T

Example JobID:19051500018

Step 3: SLiM prediction with disorder and conservation masking

Add information on conservation masking: GOPHER and OrthDB selection

http://rest.slimsuite.unsw.edu.au/slimfinder&uniprotid=jobid:19051500006:uniprot&dismask=T&consmask=T&orthdb=yeasts

Example JobID:19051500021

Step 4: QSLiMFinder prediction with a known query

The CDC9-POL30 interaction can be considered as a high quality binary interaction as it is supported by PDB structure 2OD8. This information can be used to restrict the motif search space to be in CDC9 (P04819):

http://rest.slimsuite.unsw.edu.au/qslimfinder&seqin=jobid:19051500018:seqin&dismask=T&query=P04819

Example JobID:19051500028

Step 5: QSLiMFinder prediction with a known query region

Chain B of 2OD8 is a 22 aa segment of P04819: region 32-53. This can be given to qslimfinder to further increase the sensitivity:

http://rest.slimsuite.unsw.edu.au/qslimfinder&seqin=jobid:19051500018:seqin&dismask=T&query=P04819&qregion=32,53

Example JobID:19051500029

NOTE: The qregion setting has been updated and is now based on a 1 to Length numbering. Multiple regions can be give by separating with commas, e.g. qregion=1,10,32,53 would keep region 1-10 and region 32-53.