SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks

@article{Olorin2015SLiMScape3A,
  title={SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks},
  author={Emily Olorin and Kevin T. O'Brien and Nicol{\'a}s Palopoli and {\AA}sa P{\'e}rez-Bercoff and Denis C. Shields and Richard J. Edwards},
  journal={F1000Research},
  year={2015},
  volume={4}
}
Short linear motifs (SLiMs) are small protein sequence patterns that mediate a large number of critical protein-protein interactions, involved in processes such as complex formation, signal transduction, localisation and stabilisation. SLiMs show rapid evolutionary dynamics and are frequently the targets of molecular mimicry by pathogens. Identifying enriched sequence patterns due to convergent evolution in non-homologous proteins has proven to be a successful strategy for computational SLiM… 

Figures and Tables from this paper

FlexSLiM: a Novel Approach for Short Linear Motif Discovery in Protein Sequences
TLDR
FlexSLiM provides a general tool that will advance the understanding of short linear motifs, which will facilitate the research on protein targeting signals, protein post-translational modifications, and many others.

References

SHOWING 1-10 OF 27 REFERENCES
SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context
TLDR
The SLiMSearch webserver is a flexible tool that enables researchers to identify novel occurrences of predefined SLiMs in sets of proteins, and provides user-friendly output and visualizations of motif context to gain insight into the validity of a putatively functional motif occurrence.
SLiMScape: a protein short linear motif analysis plugin for Cytoscape
TLDR
SLiMScape provides a platform for performing short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment.
SLiMSearch 2.0: biological context for short linear motifs in proteins
TLDR
The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences.
The SLiMDisc server: short, linear motif discovery in proteins
TLDR
The SLiMDisc (Short, Linear Motif Discovery) web server corrects for common ancestry in describing shared motifs, concentrating on the convergently evolved motifs.
QSLiMFinder: improved short linear motif prediction using specific query protein data
TLDR
QSLiMFinder exploits prior knowledge of a query protein likely to be involved in a SLiM-mediated interaction to increase the sensitivity and specificity of predictions and reduce the proportion of datasets returning a false positive prediction.
Computational prediction of short linear motifs from protein sequences.
TLDR
This review explores the current knowledge of SLiMs and how it can be applied to the task of predicting them computationally from protein sequences and highlights the importance of correctly modelling evolutionary relationships and the probability of false positive predictions.
Interactome-wide prediction of short, disordered protein interaction motifs in humans.
TLDR
Although not as compositionally biased as previous studies, patterns matching known SLiMs tended to cluster into a few large groups of similar sequence, while novel predictions tended to be more distinctive and less abundant.
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
TLDR
The TEIRESIAS algorithm was shown to significantly outperform methods that do not discount evolutionary relatedness, when applied to known SLiMs from a subset of the eukaryotic linear motif (ELM) database, and an implementation of Multiple Spanning Tree weighting outperformed two other weighting schemes, in a variety of settings.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
TLDR
Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
TLDR
A new method is developed that assesses the evolutionary signal of a residue in its sequence and structural context and incorporation into the existing statistical model employed by SLiMFinder is allowed, indicating that it could be of general benefit to computational annotation and prediction of protein function at the sequence level.
...
...