A worldwide e-Infrastructure for NMR and structural biology

Website usage Issues

Regarding HADDOCK scores

Dear all,

I used HADDOCK to dock my proteins. The result shows different clusters, which we can choose by the HADDOCK score. The top cluster has 4 best structures. Now my question is how to select the best from these 4 structures.

1) Do I have to look into the  individual scores (Desolvation energy, Binding energy, Internal energy complex etc.) of each 4 structures?

2) Does the Internal energy compleex means vdw and elec energy?

 

 I cannot access the full paper of HADDOCK, so I am not able to understand the details. Kindly help me.

Issue status: 
Closed

Unexpected and non-informative error message

Hello,

 

I have been docking a transcription factor that was co-crystallized with DNA, submitting the active residues as outlined in the accompanying paper. However, my HADDOCK run fails with the following error message (in the HADDOCK output file, see attached file):

 

HADDOCK cannot continue due to failed structures in it1
HADDOCK could not copy failed structures from previous iteration
The following structures could not be docked: 
    [76]

 

Issue status: 
Open

publications and presentations

Hi there,

i would propose to have in the menu "about us/project" the choice publications and presentations besides the current items deliverables, fact sheet and eNMR & WeNMR. It should collect all the WeNMR-related publications and talks given at the conferences on behalf of WeNMR (or their links to them), maybe made accessible only to users registered with the portal ,as done e.g. in http://www.euindiagrid.eu/index.php/pubblications-doc.

Issue status: 
Closed

Help center post subscriptions

How can I see to which post of the help center I am subscribed to and the frequency of email?

Issue status: 
Closed

FAQ

 

Frequently Asked Questions

 

Issue status: 
Open

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life