ELMotiSt - Eukaryotic Linear Motifs Structure

The Eukaryotic Linear Motif database (ELM) is 'a repository of annotated motif data and an exploratory tool for motif prediction'. ELMs are a subset of the short protein segments involved in protein-protein interactions commonly known as Short Linear Motifs (SLiMs). They are enriched in intrinsically disordered regions of proteins but it is generally neglected that three-dimensional structure may play a key part in functionality, at least for certain SLiM classes.

ELMotiSt is a utility for studying structural features in ELMs. It uses the 'elm_instances.[date].tsv' file generated by SLiMSuite to link and tabulate ELM information, UniProt mapping, instances in PDB, etc. A parsed file of SIFTS annotations is used for mapping ELMs onto PDB:Chain. It collects structure information from available PDBs and from computational prediction software.

Usage

This wiki is intended to serve as internal documentation during the development of the scripts used to collect, parse and analyse the data generated mainly for the ELM structure assessment paper. It consists of just one page. This and all documentation in the main repository are encoded in basic Markdown syntax.

Use the sections below to track all changes and issues you may come across when working with these files. Description of the analyses, scripts, results and relevant information for the paper should not be placed here; use the 'doc' folder in the main repository instead.

Paper

Structural properties of Short Linear Motifs. Nicolas Palopoli, Richard J. Edwards, Gustavo Parisi, Cristina Marino-Buslje. (working title; in preparation)

External Resources

QSLiMFinder Manual
PDB secondary structure annotations
PDB disorder annotations

Latest News

• 13-11-2015: First version of the wiki released.

Known Issues and To-Do

#1: Arguments parsing in ELMotiSt.py does not tolerate errors.

[ ] : Replace argument parsing with argparse

#0: Template. Description of problem.

[ ] : Template. Description of issue.