PSVS

Running the PSVS Server

PSVS (protein structure validation server) systematically evaluates the quality of protein structures. PSVS reports a set of quality scores and constraint analyzes. PSVS defines a set of standard quality scores and constraint analyses that are reported for each structure. In addition to experimental constraints, this set encompasses a number of parameters evaluating different aspects of structure quality, including fold and packing, local residue separation, deviations of bond length and bond angles, backbone and side-chain torsion angle conformation, and atomic overlaps. Quality scores are reported based on calibration with a set of high-resolution X-ray crystal structures. A Z-score for the query structure, calculated for the score from each tool, provides an evaluation of the quality of the structure compared to this set of X-ray crystal structures. This server returns a concise validation report that includes a standard set of graphs and tables.

Submitting data for PSVS check

Once the structure available, go to the PSVS server and upload the input files as described in that page:

• PDB coordinates: atom names can be in PDB format, DYANA/CYANA or CNS/XPLOR format
• Peak lists (optional, for RPF scores check): separate peak lists from 15N-resolved NOESY and 13C-resolved NOESY.
• Chemical shift (optional, for constraints violation and RPF scores check): BMRB 2.1 format
• Constraints (optional, for constraints violation check): can be CYANA or CNS format.

*PSVS Output*

One will get an e-mail notice a few minutes after PSVS submisson, following the link in the e-mail will lead to the PSVS results

• Secondary Structure Elements
• Ordered residues
• RMSD values for all residues and ordered residues.
• Ramachandran Plot Summary for ordered residues from Procheck
  • Global quality scores for Verify3D, ProsaII, Procheck (phi-psi), Procheck (all) and MolProbity Clashscore. It is required that one should never deposit a structure to the PDB with Z scores < -5 for Procheck scores and Molprobity clashscores. General, Z szores > -3 for both Procheck G factor and Molprobity Clashscore are recommended.
  • RPF Scores (optional). A good structure should have R > 90%, P > 90%, F> 90% and DP > 70%.

-- Main.GaohuaLiu - 05 Feb 2007