WP2

Scientific focus

– IDP Function classification

Objectives

WP2 will try to establish the best possible classification of different IDP phenomena and solve detection issues. IDPs are associated to many different protein functions that are very well described in the literature but not codified as part of a structured ontology or vocabulary (e.g. Gene Ontology). Preliminary attempts have been implemented, but a better description and integration with existing ontologies is required. Experimental IDP detection is always indirect (e.g. missing electron densities from X-ray, flexibility in NMR models) and different types of experiments represent different levels of evidence.

Task list

WP Information

WP type:

research

Duration:

M7 – M57

Person months:

WP leader:

EOTVOS, Zsuzsanna Dosztanyi

Task 2.1 – IDR functional ontology: generating ontology terms and descriptions both for IDP function and experimental detection methodologies using the OBO standards.
Task 2.2 – IDR low complex overlap: Detection of short linear motifs from structure is complicated. Simple pattern search generates lot of false positives (FPs) since they are very short (ca. 5 residues). The task will provide new strategies to limit FPs by filtering matches localized to buried residues outside linear structural stretches.
Task 2.3 – IDR types from sequence: an analysis of the relationships between IDPs and sequence low-complexity and repetition.
Task 2.4 – IDP evolution: an explanation of the mechanisms driving IDP evolution.

Deliverables

D2.1

Software package for the automatic extraction of PED entry data from protein ensembles
[Confidential document – Submitted on 31/08/2019]

D2.2

Software for automatic detection of IDRs and linear motifs from protein structures