View source for PSVS

== '''Introduction'''  ==

[https://montelionelab.chem.rpi.edu/PSVS/ PSVS] (Protein Structure Validation Server) systematically evaluates the quality of protein structures, and reports a large set of quality scores and constraint analyses [1]. 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.&nbsp; <br> 

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== '''Running the PSVS server'''  ==

Once the structure is available, go to the [https://montelionelab.chem.rpi.edu/PSVS/ PSVS server] and upload the input files as described in that page (Figure 1).<br> 

*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 <sup>15</sup>N-resolved NOESY and <sup>13</sup>C-resolved NOESY. 
*Chemical shift (optional, for constraints violation and RPF scores check): BMRB 2.1 or 3.1 format 
*Constraints (optional, for constraints violation check): can be in CYANA or XPLOR/CNS format.

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===== Figure 1:&nbsp; PSVS 1.4 input page  =====

[[Image:PSVS1.4 titlepage.png|800px]] 

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== '''PSVS Output'''  ==

One will get an e-mail notice a few minutes after PSVS submisson, and following the link in the e-mail will lead to the PSVS results (Figure 2).&nbsp; Various outputs can be accessed from tabs in the left margin, and a zipped file of the entire analysis can be downloaded.<br> 

Typical PSVS&nbsp;analyses include: 

*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 [http://nihserver.mbi.ucla.edu/Verify_3D/ Verify3D], [http://www.came.sbg.ac.at/Services/prosa.html ProsaII], [http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html Procheck] (phi-psi), Procheck (all) and [http://molprobity.biochem.duke.edu/ MolProbity] Clashscore. It is required that one should never deposit a structure to the PDB with Z scores &lt; -5 for Procheck scores and Molprobity clashscores. General, Z szores &gt; -3 for both Procheck G factor and Molprobity Clashscore are recommended. 
**RPF Scores (optional). A good structure should have R &gt; 90%, P &gt; 90%, F&gt; 90% and DP &gt; 70%.

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===== Figure 2:&nbsp; PSVS 1.4 output page  =====

[[Image:PSVS1.4_outputpage_new2.png|1000px]]<br> 

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== '''References'''  ==

[http://www3.interscience.wiley.com/journal/114029977/abstract 1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. ''Proteins 66'', 778-795.]