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. 2003 Jul 1;31(13):3316-9.
doi: 10.1093/nar/gkg565.

VADAR: a web server for quantitative evaluation of protein structure quality

Leigh Willard  1 , Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F Boyko, Brian D Sykes, David S Wishart
Affiliations

VADAR: a web server for quantitative evaluation of protein structure quality

Leigh Willard et al. Nucleic Acids Res. .

Abstract

VADAR (Volume Area Dihedral Angle Reporter) is a comprehensive web server for quantitative protein structure evaluation. It accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input and calculates, identifies, graphs, reports and/or evaluates a large number (>30) of key structural parameters both for individual residues and for the entire protein. These include excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality. These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar.

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Figures

Figure 1
Figure 1
A screenshot montage of VADAR output for thioredoxin (2TRX) showing an example of the Ramachandran plot, the MAIN (main chain) tables and the 3D profile plot (quality index). 2TRX is a good example of a high quality, high resolution structure.
See this image and copyright information in PMC

References

    1. Westbrook J., Feng,Z., Chen,L., Yang,H. and Berman,H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489–491. - PMC - PubMed
    1. Kabsch W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577–2637. - PubMed
    1. Vriend G. (1990) WHAT IF: A molecular modeling and drug design program. J. Mol. Graph., 8, 52–55. - PubMed
    1. Morris A.L., MacArthur,M.W., Hutchinson,E.G. and Thornton,J.M. (1992) Stereochemical quality of protein structure coordinates. Proteins, 12, 345–364. - PubMed
    1. Baker E.N. and Hubbard,R.E. (1984) Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol., 44, 97–179. - PubMed

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