SLiMAn v2.6
Short Linear Motif Analysis

Description

SLiMAn is a free access webserver devoted to analysis of interactomic results, to suggest interactions involving Short Linear Motif (SLiM) paired with structured domain within the submited list of putative interactants. SLiMs are usually defined as short segments (< 25 residues) in a polypeptide harboring a signature recognized by a family of folded domains (e.g.: polyproline stretches and SH3 or WW domains).

From a simple list of proteins (Uniprot Acc/Ids), SLiMAn will process the data with 3 successive levels of analysis named: SLiMAn-Pairings, SLiMAn-Alignments and SLiMAn-Modeling.

Learn more about all the functionalities in the documentation section or in the user manual and from the published research articles describing the first version Reys & Labesse, Journal of Proteomic Research (2022) and SLiMAn2 Reys et al, Nucleic Acids Research (2024).
A thorough description of the usage of SLiMAn2 is available in a coming issue of Method Mol. Biol., where an extensive application on the analysis of human tankyrase interactome is provided as an illustrative example. A draft is available at: https://www.researchsquare.com/article/rs-3973092/v1

This website is free and open to all users and there is no login requirement.

Usages

There are two main types of inputs:

Submit your own interactome:

Project Name


Uniprot List (must be separated by comma)

and / or
Uniprot File

Open Access
Compute PubMed Co-occurences


  • Enter your project name
  • Input section?:
    → Uniprot list : Add by hand a list of Uniprot Accession/Identifiers separated by a comma
    → Uniprot file : Upload a file containing your list of Uniprot Accession code as would be presented in the header of a FASTA format(>sp|Acc|SuppDt ... ) ?
  • By checking Open Access, your project will be accessible from the listing in webserver results
  • By checking Compute PubMed co-occurences, number of co-occurences in research papers are retrieved from the PubMed API (please, consider using this option for small interactomes only?)
  • Optionally, define your own classes with their corresponding regular expression
  • Press "Find Interactions" to start SLiMAn

Click this button to set the FRAT2 input example

Search for a (meta)-interactome:

This input section aims are retrieving a meta-interactome from protein-protein interaction databases. This search will highlight a list of interactants from BioGRID and/or IntAct. Parameters can be adjusted to narrow down the enlisted proteins before submitting the analysis using a dedicated Quick launch button.

UniProt Accession / Identifier


BioGRID
InAct


  • A Uniprot accession/identifier
  • Check the databases used for the search
  • Press "Find Interactants" to search for partners currently referenced in the selected databases

Access to computed results:

This input section aims are retrieving a results obtained from a previous SLiMAn query.

Project Name



SLiMAn2 precomputed examples

FRAT2 Interactome (14 proteins)
Pragmin Interactome (62 proteins)
GIPC1 meta-interactome (96 proteins)

SLiMAnDB

SLiMAn has its own structural database extracted from the PDB to provide templates for internal homology modeling (SLiMAn-Modeling procedure). This database contains a subset of PDB structures corresponding to complexes having a peptide containing an ELM motif in proximity to a Pfam domain. The current database contains 5325 structures of protein-peptide complexes.
The database is accessible as is using this download link (244 Mo).

Current Release

SLiMAn build : 2.6.08022023
DataBases last update : 2025-03-06 11:16:12
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