Description

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SLiMAN is a webserver devoted to analysis of interactomic results, to suggest possible ELM/PFam pairs within the submited list of putative interactants.

From a simple list of Uniprot Acc/Ids, SLiMAN will process the data with 3 successive levels of analysis named : SLiMIP, SLiMID and SLiMIM. These three steps are described below.

SLiM-IP : Short Linear Motif Interaction Prediction

For each of the input UniProt ID, regular expressions from the linear motifs referenced in the database ELM are used to parse de corresponding sequences. In parallel, PFam domains are matched to the same set of sequences. SLiMIP gather complementary information from Uniprot, ELM, IUpred2, BioGrid and PhosphoSitePlusⓇ.

SLiMIP draws a table indicating possible pairings with information for each hit :
-> Associated PFam ID
-> ELM class name
-> ELM motif class E-value
-> ELM experimentaly validated matchs (Verified Instances)
-> IUpred2 motif disorder scores
-> BioGrid data for the association of two Unicodes
-> PhosphoSitePlusⓇ PTMs
-> SLiMID available templates count

Parameters can be modified interactively (e.g. : E-value, Disorder) to filter the hits from the output lists of putative pairs.
In addition, SLiMIP provides direct links to the corresponding information pages from PFam, ELM, and PhosphoSitePlus webservices. When possible, a link to potential templates for a ELM/PFam pair is provided.

SLiM-ID : Short Linear Motifs Interracting with Domains

SLiMID highlights the ELM motif and the match PFam domain withing the paired sequences, and alignments with potential templates. The latter were extracted from PDB structures and constitute a database of 3D information for the 291 ELM/PFam associations.
The current database contains 5064 3D structures (extracted from 2228 PDB entries) of protein-peptide complexes to serve as templates to model hits sharing the same ELM/PFam elements.
The motifs boundaries can be edited for the ELM motif and the PFam domain. Sequences identity and sequence coverage of the alignment is provided to help in the selection of the suitable templates. Residues belonging to the protein-peptide interface are colored (red/orange/green for contact distances of 4/5.5/7 Angstroms).
Each alignment can be selected for modeling the 3D complex using SCWRL3.0. SLiMIP hits can be visualized as sequences, and alignments with corresponding SLiMID templates are performed.

SLiM-IM : Short Linear Motifs Interaction Modeling

From the alignments selected in SLiMID, a model of the complex is performed in two steps.
First, the variable side-chains of the PFam domain are modeled using SCWRL in the presence of the peptide found in the template.
Then, the new queried peptide sequence is modeled also with SCWRL 3.0 in the presence of the new modeled PFam domain. Generated models are deduced from the alignments performed by BLASTⓇ or MAFFT.

The 3D models of the complexes can be visualized using JSmol applet or downloaded in PDB format. Each model can be selected or discarded. Such selection is forwarded to SLiMIP results display.

Usage

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SLiMAN query

I. Project Name : Enter your project name

II. Input section :
-> Uniprot file : Upload a file containing your list of Uniprot ACC as would be presented in the header of a FASTA format (input example).
-> Uniprot list : Add by hand a list of Uniprot ACC|ID separated by a comma (input example).

III. Press "Find Interactions" and enjoy data analysis :)

BioGrid query

I. Input section :
-> Uniprot file : Upload a file containing your list of Uniprot ACC as would be presented in the header of a FASTA format (>sp|ACC|SuppDt ... )
-> Uniprot list : Add by hand a list of Uniprot ACC|ID separated by a comma

II. Press "Find Interactions" to find interactants currently referenced in BioGrid

-> Full documentation HERE <-

Examples

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Published Examples

Query : BRAF_HUMAN, 1433(B,E,F,G,S,T,Z)_HUMAN
Results : HERE

Query : FRAT2_HUMAN, GSK3B_HUMAN, XPO1_HUMAN, + 11 BioGRID interactants
Results : HERE

Query : Pragmin + 61 interactants
Results : HERE

Examples with modified parameters

B-RAF interactors from BioGrid (2 or more detections)

ERBIN interactors from BioGrid (2 or more detections)

CSK interactors from BioGrid (1 or more detections)

PLK1 interactors from BioGrid (1 or more detections)

14-3-3 (Default)

14-3-3 (BioGrid >= 1 ; Input Order)

14-3-3 (BioGrid >= 1 ; Cluster Order)

14-3-3 (BioGrid >= 2)

Degradation Sites

Current Release

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SLiMAN Version : 1.952
DataBase last update : 2021-07-05 11:14:20