The Structure Analysis and Verification Server version 4



[SAVES] • XdValMTZdumpRamachandran PlotpdbProbepdbSNAFU (Check for ADIT compliance)

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

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 assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. [Reference]
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. [Reference]
CRYST1 record matchesNew. We take the CRYST1 record and search the entire PDB for matches and report these as possibly similar structures.

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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SAVES version 3 is located here



If you find anything not running properly, please email me holton@mbi.ucla.edu

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