A worldwide e-Infrastructure for NMR and structural biology

Getting started with FANDAS

The FANDAS (Fast Analysis of multidimensional NMR DAta sets) program generates chemical shift predictions for a range of 2D and 3D solid-state NMR experiments. As these predictions are always based on an amino acid sequence, the program is restricted to protein/peptide samples. However, it is possible to incorporate additional data information like experimental NMR chemical shift assignments, in-silico data produced by computational procedures (e.g. ShiftX) or different labeling schemes. The final output file can be read in as a peak list the Sparky software. Using the server is easy and only requires 3 steps:

Step 1. Access to the server

The FANDAS server is a utility server and does not perform any calculations on the grid, a grid certificate is thus not required. FANDAS performs the predictions almost instantaneously and uses the current browser session to keep track of all predictions made. It is therefor not needed to login to the server, you may use it right away.

 

Step 2. Starting a prediction (step 1 on the server interface)

Enter a protein sequence and optional secondary structure prediction as start point of the prediction. Enter a file name for this prediction so you can keep track of it while using one or more of the 30 prediction tools available.

 

Step 3. Optionally modify the input provided at the previous step (step 2 on the server interface)

You may modify the input you provided in the previous step to account for different labeling schemes, fractional deuteration or reading BMRB tables. Provide a new filename for every modification you make so you always have the original input and the modified input at hand. This way of working also allows you to perform multiple modifications (and predictions later on) on the same data. 

 

Step 4. Perform the spectrum predictions (step 3 on the server interface)

With the (modified) input data available in your session you may start using any of the 30 prediction tools. They predict spectra for several 2D and 3D experiments and present there output in Sparky format. As with the previous step, all generated files remain available in your session. Your session remains valid for as long as you have your browser open at the FANDAS interface. 

 

0
Your rating: None

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