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The UCLA-DOE Structure Evaluation server is a tool designed to help in the refinement of crystallographic structures. It will provide you with a visual analysis of the quality of a putative crystal structure for a protein. Verify3D expects this crystal structure to be submitted in PDB format. Please note that Verify3D works best on proteins with at least 100 residues. To submit a crystal structure for analysis, simply select it with the file dialog which is activated by clicking on the Browse button below, then click the Send File button.
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Verify3D analyzes the compatibility of an atomic model (3D) with its own amino acid sequence (1D). Each residue is assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar, etc). A collection of good structures is used as a reference to obtain a score for each of the 20 amino acids in this structural class. The scores of a sliding 21-residue window (from -10 to +10) are added and plotted for individual residues.
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References:
[Bowie et al., 1991;
Luethy et al., 1992].
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