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ASDP

ASDP is an automated NMR NOE assignment engine. It uses a distinct bottom-up topology-constrained approach for iterative NOE interpretation and generates 3D structures of the protein that is as close to the true structure as possible.ASDP first builds an initial chain fold based on intraresidue and sequential NOESY data, characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unambiguous long-range NOE interactions, based on chemical shift matching and NOESY spectral symmetry considerations. "Ambiguous constraints" are not used in the initial structure calculations.ASDP generates distance constraint lists and utilizes the program Xplor for 3D structure generation. DP scores are calculated for all intermediate models. Only the top models with highest DP scores and lowest conformational energy (XPLOR) values are selected for iterative NOE analysis. After two cycles of model generation with XPLOR and model selection with DP filter, NOESY cross peaks are iteratively assigned using the intermediate 3D structures and contact maps, together with knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models.

 


 

Precomputed results (zip file) *

 

Fill in the fields below and click submit.  
Protein Name: *
Email: *
Model Builder: Xplor
Number of Cycles:
BMRB:
Dihedral Constraints:
2D NOESY
3D 15N NOESY
3D C13 aro
d2O Solution
3D C13 ali
d2O Solution
Water suppr: ppm-ppm
3D C13 NOESY
d2O Solution
Water suppr: ppm-ppm
4D C-C NOESY
d2O Solution
Water suppr: ppm-ppm
* Required parameters

 

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