The Structure Analysis and Verification Server version 4
[SAVES] • XdVal • MTZdump • Ramachandran Plot • pdbProbe • pdbSNAFU (Check for ADIT compliance)
This metaserver runs 6 programs for checking and validating protein structures during and after model refinement.
| 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 assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. [Reference] |
| 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. [Reference] |
| CRYST1 record matches | New. 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 |
SAVES version 3 is located here
If you find anything not running properly, please email me holton@mbi.ucla.edu
* Jobs are removed every Sunday morning at 2AM Pacific time *
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