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Nucleic Acids Research, 2003, Vol. 31, No. 13 3316-3319
© 2003 Oxford University Press

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

Leigh Willard, Anuj Ranjan1, Haiyan Zhang1, Hassan Monzavi1, Robert F. Boyko, Brian D. Sykes and David S. Wishart*,1

Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2N8, Canada 1 Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2N8, Canada

*To whom correspondence should be addressed. Tel: +1 7804920383; Fax: +1 7804925305; Email: david.wishart{at}ualberta.ca

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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