VADAR molecules image

Single (or Multiple) Model Protein Structure Analysis



VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data. The results have been validated through extensive comparison to published data and careful visual inspection.  The VADAR web server supports the submission of either PDB formatted files or PDB accession numbers.  VADAR produces extensive tables and high quality graphs for quantitatively and qualitatively assessing protein structures determined by X-ray crystallography, NMR spectroscopy, 3D-threading or homology modelling. 

Please cite the following: Leigh Willard, Anuj Ranjan,Haiyan Zhang,Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, and David S. Wishart "VADAR: a web server for quantitative evaluation of protein structure quality" Nucleic Acids Res. 2003 July 1; 31 (13): 3316.3319

We have another advanced server for detecting the quality of protein structure. www.resprox.ca

Acknowledgements:
We would like to thank PENCE and CIHR for their financial support.

 
For additional information on how to run VADAR click this button
 
Select desired PDB file
Note: the uploaded file must be in PDB format in order for this form to work. Refer to the HELP button above.
OR Enter PDB accession number
(Please specify the chain e.g. 4TRXA (4TRX chain A), If not specified, all chains will be processed, e.g. 4TRX)


Program Options:
  1. Calculate hydrogen bonds to water
  2. Values for Van der waals radii
    • Chothia
    • Eisenberg
    • Richards
    • Shrake
  3. Take definition of polar/nonpolar ASA and charged ASA from
    • Chothia
    • Eisenberg
    • Shrake
  4. Type of volume calculation
    • Standard Voronoi procedure>
    • Richards Method B
    • Radical Plane procedure
Table Output Options:
Main Chain Information
Side Chain Information
Hydrogen Bond Information
Quality Index Information
Statistics Information

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