This metaserver runs 6 programs for checking and validating protein structures during and after model refinement.
This server processed 2,818.2 jobs per month in the last 12 months. See more usage statistics here
|PROCHECK||Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [Reference]|
|WHAT_CHECK||Derived from a subset of protein verification tools from the WHATIF program (Vriend, 1990), this does extensive checking of many sterochemical parameters of the residues in the model. [Reference]|
|ERRAT||Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures. [Reference]|
|VERIFY_3D||Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. References: [Bowie et al., 1991; Luethy et al., 1992].|
|PROVE||Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and calculates a statistical Z-score deviation for the model from highly resolved (2.0 Å or better) and refined (R-factor of 0.2 or better) PDB-deposited structures. [PUBMED Reference].|
|CRYST1 record matches||We take the CRYST1 record and search the entire PDB for matches and report these as possibly similar structures.|
|Ramachandran Plot||We produce an interactive Ramachandran plot. Also a standalone server linked above.|
|WedMol Viewer||We provide a structure viewer in the web page, although not all browsers support it. We are working to pvoride a more robust viewer|
A user can run all 6 programs to get a collective view of the input structure, or individual programs can be selected.
The evaluations the server makes of the outputs of each program are labeled by a simple 3 color scheme: