[3dem] NMR resources at PDBe (pdbe.org/nmr)

Thu Jul 14 12:02:58 PDT 2011

Hi all,

[I realise this is off-topic. However, one day you may need to fit an NMR 
model to an EM map. When that day comes, it will be good to know that you can 
find useful validation-related information as well as representative models at 
PDBe.]

The Protein Data Bank in Europe (PDBe; http://pdbe.org/) continues to improve 
its services to the scientific community. As part of our recent website update, 
we have reorganised and simplified the way information about NMR entries is 
shown. We have also released Vivaldi (Visualisation and Validation Display; 
http://pdbe.org/vivaldi), an interactive tool that allows you to inspect 
available validation reports and check for restraint violations or RDC fits. 
For an example, try http://pdbe.org/vivaldi/2keo

The pages describing the NMR resources at PDBe (http://pdbe.org/nmr) have been 
revised and streamlined. They allow you to search the VASCO, OLDERADO, RECOORD 
and logRECOORD databases (see below) and also provide information about 
deposition of NMR structures and accompanying data, as well as some work 
related to the CCPN framework. The NMR statistics page shows the current status 
of NMR-related information in the PDB and at PDBe 
(http://www.ebi.ac.uk/pdbe-apps/nmr/statistics).

On the PDBe atlas pages of a particular NMR entry (e.g., http://pdbe.org/2keo - 
cytochrome-b5-like domain of the HERC2 E3 ligase - or try 
http://pdbe.org/hasnmr for a randomly picked NMR entry), you can access 
available experimental information by clicking on the "Experiment" link in the 
navigation menu on the left of the page. Alternatively, whenever you see a 
PDBprint (http://pdbe.org/pdbprints) for an NMR entry, you can click on the 
"NMR" icon to get to the NMR experimental information page. Finally, if you 
know the PDB code, you can go there directly (e.g., 
http://pdbe.org/2keo/experimental). When you click a "View" link in the table 
on the experimental information page, it will redirect you to a predefined 
Vivaldi view (e.g., restraints or validation reports).

The experimental information page allows you to navigate to the corresponding 
Biological Magnetic Resonance Bank (BMRB) entry containing assigned chemical 
shifts. (Note: experimentally determined chemical shifts are now mandatory when 
depositing NMR structures). Sometimes, more than one BMRB entry relates to the 
same PDB entry, for instance in the case of close homologues or alternate 
protein constructs (>97% sequence identity). You can download deposited 
restraints from the PDB archive or navigate to the remediated restraints from 
the NMR Restraints Grid (NRG) at BMRB. For most NMR entries there is an 
in-depth validation report from the NRG-CING database, hosted at the Radboud 
University of Nijmegen.

VASCO - Validation of assigned chemical shifts through coordinates - is a 
database of 2000+ validation reports, which can be downloaded as text files or 
viewed interactively in Vivaldi. OLDERADO reports on domain composition, 
clustering and representative models of a deposited ensemble are available for 
most NMR entries that contain proteins. They can be viewed in Vivaldi or in a 
tabular format. Two databases of recalculated ensembles are hosted by PDBe: 
RECOORD, with 500+ entries, which compares four common structure-determination 
protocols, and logRECOORD, with 300+ entries, which uses a "log-normal" 
potential for interpreting NOE data.

Finally, you may be interested in some recent NMR-related papers co-authored by 
current and former PDBe staff:

1. Lemak et al., "A novel strategy for NMR resonance assignment and protein 
structure determination", Journal of Biomolecular NMR 49, 27-38, 2011 
(http://dx.doi.org/10.1007/s10858-010-9458-0)

2. Bernard et al., "Bayesian estimation of NMR restraint potential and weight: 
a validation on a representative set of protein structures", Proteins 79, 
1525-1537, 2011 (http://dx.doi.org/10.1002/prot.22980)

3. Penkett et al., "Straightforward and complete deposition of NMR data to the 
PDBe", Journal of Biomolecular NMR 48, 85-92, 2010 
(http://dx.doi.org/10.1007/s10858-010-9439-3)

4. Fogh et al., "MEMOPS: data modelling and automatic code generation", Journal 
of Integrative Bioinformatics 7, 123, 2010 
(http://dx.doi.org/10.2390/biecoll-jib-2010-123)

5. Rieping & Vranken, "Validation of archived chemical shifts through atomic 
coordinates", Proteins 78, 2482-2489, 2010 
(http://dx.doi.org/10.1002/prot.22756)

We hope that expert and non-expert users alike will find the NMR resources at 
PDBe useful. As always, we welcome constructive criticism, comments, 
suggestions, bug reports, etc. through the feedback button at the top of any 
PDBe web page.

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard at ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin at ebi.ac.uk