NIH MBI Laboratory for Structural Genomics and Proteomics
Please use Version 4 (2012), it is much nicer!
After browsing and selecting your input file, click on a button to run that server alone, or click on
to run some or all of them.
Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [
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. [
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. [
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. [
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. [
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holton at mbi. ucla. edu