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DANGLE
======


.. |pulldown| image:: ../images/pulldown.png
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.. |check| image:: ../images/check.png
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.. |radio| image:: ../images/radio.png
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.. |float| image:: ../images/float.png
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.. |int| image:: ../images/int.png
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.. |entry| image:: ../images/entry.png
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.. |button| image:: ../images/button.png
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.. |ramp| image:: ../images/ramp.png
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.. |selector| image:: ../images/selector.png
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**A Bayesian inferential prediction method for protein backbone dihedral angles**

DANGLE (Dihedral ANgles from Global Likelihood Estimates) predicts protein
backbone Phi and Psi angles and secondary structure assignments solely from
amino acid sequence information, experimental chemical shifts and a database
of known protein structures and their associated shifts. This approach
uses Bayesian inferential logic to analyse the likelihood of conformations
throughout Ramachandran space, paying explicit attention to the population
distributions expected for different amino acid residue types.

Simple filtering procedures can identify the most "predictable" residues,
yielding 92% of all Phi and Psi predictions accurate to within +/-30 degrees.
In contrast to previous approaches, more than 80% of Phi or Psi predictions
for glycine and pre-proline are reliable. Furthermore, DANGLE provides
meaningful upper and lower bounds for the predictions which are shown to
represent the precision of the prediction. Over 90% of the experimental
dihedral angles in the set of test proteins are within the boundary ranges
suggested by DANGLE. At a lower resolution level, the program correctly
assigns each residue to one of three secondary structure states (H, E or C) in
85% of cases.

DANGLE also provides an indication of the degeneracy in the relationship
between shift measurements and conformation at each site.

For more documentation see the `DANGLE web site`_ at SourceForge.

.. _`DANGLE web site`: http://dangle.sourceforge.net/

**Reference**

*Ming-Sin Cheung, Mahon L. Maguire, Tim J. Stevens, and R. William Broadhurst.
"DANGLE: A Bayesian inferential method for predicting protein backbone
dihedral angles and secondary structure." Journal of Magnetic Resonance Volume
202, Issue 2, February 2010, Pages 223-233*



Main Panel
==========


Options
~~~~~~~


|pulldown| **Chain**: Choose the molecular system chain to make predictions for

|pulldown| **Shift List**: Select the shift list to take input chemical shifts from

|pulldown| **Max No. of Islands**: Select the maximum allowed number of disontinuous prediction islands

|pulldown| **Dangle Run**: Select a run number to store DANGLE results within

|pulldown| **Ensemble**: Select the structure ensemble for superimposition of angle values on the GLE plots

|pulldown| **Restraint Set**: Select the CCPN restraint set to store DANGLE dihedral angle restraints in

Global Likelihood Estimates
~~~~~~~~~~~~~~~~~~~~~~~~~~~





Scrollbar: : 

|button| **Previous**: Show GLE plot of angle predictions for previous residue in chain

|button| **Next**: Show GLE plot of angle predictions for next residue in chain

Dihedral Angle Predictions
~~~~~~~~~~~~~~~~~~~~~~~~~~


=================  ===================================================================
**Table 1**
--------------------------------------------------------------------------------------
        *Res Num*  Residue number in chain 
       *Res Type*  Residue type code 
 *No. of Islands*  Number of high scoring discontinuous angle predictions 
             *SS*  Predicted secondary structure code 
            *Phi*  Predicted phi dihedral angle (CO-N-CA-CO)  *(Editable)*
            *Psi*  Predicted psi dihedral angle (N-CA-CO-N)  *(Editable)*
      *Phi Upper*  Upper bound of phi angle prediction  *(Editable)*
      *Phi Lower*  Lower bound of phi angle prediction  *(Editable)*
      *Psi Upper*  Upper bound of psi angle prediction  *(Editable)*
      *Psi Lower*  Lower bound of phi angle prediction  *(Editable)*
*Chemical Shifts*  Chemical shifts used in prediction 
=================  ===================================================================



|button| **Clear Selected**: Remove the predictions for the selected residues

|button| **Run Prediction!**: Run the DANGLE method to predict dihedral angles and secondary structure

|button| **Delete Current Run**: Delete the DANGLE results stored under the current run number

|button| **Commit Restraints**: Store the angle predictions and bounds in a new CCPN dihedral angle restraint list

|button| **Commit Secondary Structure**: Store the secondary structure predictions in the CCPN project

