Building on PDBe-KB to chart and characterize the conformational landscape of native proteins

This implementation study will create infrastructure to chart the experimentally sampled
conformational diversity of native proteins by exploiting data from the PDB, augmented with
results of state-of-the-art computational tools. By integrating resources/tools, workflows will be
developed to

i) Compare and cluster different conformations adopted by homologs of the same
protein,

ii) Identify protein regions with different flexibility properties.

Pipelines will be created to characterize conformational ensembles in terms of

i) The types of motions described (thermal fluctuations; collective motions),

ii) Their functional relevance, using sequence information and functional annotations.

These data will be integrated into the PDBe Knowledge Base and presented in the aggregated views (PDBe is an ELIXIR-Core-Data-Resource), which are freely available to the scientific community. Applications of these new capabilities will be explored in a joint gap analysis with the IDP and Proteomics Communities, including joint meetings, in order to identify future implementations that best serve ELIXIR goals.

Platform/Community: 

People involved: 

nathalie_reuter
Adam Hospital
Sameer Velankar
Wim Vranken
Shoshana Wodak
Christine Orengo
antoniorosato71
Damiano Piovesan
Michael Turewicz
Lennart Martens
Sergei Grudinin
Steve Hayward
Modesto Orozco
Pablo Chacon
Marc Lensink
Kresten Lindorff-Larsen
Tamas Hegedus
Dina Schneidman
Joel Sussman