The Structure Analysis and Verification Server version 4



This metaserver runs 6 programs for checking and validating protein structures during and after model refinement.

This server processed 3,112.8 jobs per month in the last 12 months. See more usage statistics here


Monthly totals plot
PROCHECKChecks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [Reference]
WHAT_CHECKDerived 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]
ERRATAnalyzes 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_3DDetermines 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].
PROVECalculates 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 matchesWe take the CRYST1 record and search the entire PDB for matches and report these as possibly similar structures.
Ramachandran PlotWe produce an interactive Ramachandran plot. Also a standalone server linked above.
WedMol ViewerWe 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:

GOOD: SATISFACTORY
WARNING: INSPECTION SUGGESTED
ERROR: INSPECTION RECOMMENDED


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Program selecting has been temporarily removed. We are upgrading the entire server.
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* Jobs are removed every Sunday morning at 2AM Pacific time *

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