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

Leigh Willard | Zendy

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

Author(s) -

Leigh Willard

Publication year - 2003

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkg565

Subject(s) - protein data bank , dihedral angle , protein data bank (rcsb pdb) , web server , biology , steric effects , hydrogen bond , protein structure , ramachandran plot , accession , accessible surface area , crystallography , bioinformatics , computer science , database , the internet , biochemistry , world wide web , chemistry , stereochemistry , molecule , organic chemistry , european union , business , economic policy

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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