FunPDBe: Community-driven enrichment of PDB data

Structural and functional annotations

What is FunPDBe

FunPDBe is a project of the Protein Data Bank in Europe - Knowledge Base (PDBe-KB) with the goal to create an integrated and accessible resource of structural and functional annotations for macromolecular structure data in the Protein Data Bank (PDB). It is a collaboration between the PDBe-KB and world-leading providers of structural bioinformatics data.

The goal of FunPDBe

The project promotes interoperability, comparative analysis and exchange of structural and functional annotations by implementing common data standards and infrastructure to collect these enhanced annotations. PDBe-KB, of which FunPDBe is a flagship project, aims to significantly increase the impact of structural data globally by implementing a central sustainable data resource and a uniform data access mechanism (via FTP and REST API) for distribution of these valuable functional and structural annotations, developed by researchers. The data is to be made accessible via web interface by developing re-usable web components.

How to deposit data

PDBe-KB is open to deposition of annotations from potential collaborating data resource or scientific software developers. Please contact PDBe-KB for more details.


Participating resources

14-3-3-Pred Geoff Barton group http://www.compbio.dundee.ac.uk/1433pred
3D Complex Emmanuel Levy group https://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi
3DLigandSite Mark Wass group http://www.sbg.bio.ic.ac.uk/~3dligandsite/
AKID Manuela Helmer Citterich group http://akid.bio.uniroma2.it/
Arpeggio Tom Blundell group http://biosig.unimelb.edu.au/arpeggioweb/
CamKinet Toby Gibson group http://camkinet.embl.de/v2/home/
canSAR Bissan Al-Lazikani group https://cansar.icr.ac.uk/
CATH-FunSites Christine Orengo group http://www.cathdb.info/
ChannelsDB Jaroslav Koca group http://ncbr.muni.cz/ChannelsDB/
COSPI-Depth M.S. Madhusudhan group http://cospi.iiserpune.ac.in/depth
DynaMine Wim Vranken group http://dynamine.ibsquare.be/
FoldX Luis Serrano group http://foldxsuite.crg.eu/
M-CSA Janet Thornton group https://www.ebi.ac.uk/thornton-srv/m-csa/
MetalPDB Claudia Andreini, Antonio Rosato group http://metalweb.cerm.unifi.it/
Missense3D Michael Sternberg group http://www.sbg.bio.ic.ac.uk/~missense3d/
P2Rank David Hoksza group http://prankweb.cz/
POPSCOMP Franca Fraternali group http://popscomp.org:3838/
ProKinO Natarajan Kannan group http://vulcan.cs.uga.edu/prokino/about/prokino
SKEMPI Iain H Moal group https://life.bsc.es/pid/skempi2/