PSVS Documentation


Other Options:

By choosing 'Input More Infor', you can input the information which you wish to be included in your PSVS report

Format of secondary structure file:

If you prefer not to use DSSP to calculate secondary structure, you can upload a secondary structure file. The secondary structure file should conform to standard PDB format. Please refer to this webpage:
http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html

Residue range selection

When running PROCHECK analysis, you can either choose analyze all the residues or just ordered residues, for single chain protein you can even analyze any user-defined residues by selecting 'Custom' option. In this case, you should upload a residue range file, which should be formatted as the following:
1A-15A
20A-70A

RPF analysis

You need to upload peak list file and chemical shift file to run RPF analysis, which would output NMR quality assessment scores, including Recall, Precision, and F-measure scores (referred to here are NMR RPF scores), which quickly provide global measures of the goodness-of-fit of the 3D structures with NOESY peak lists using methods from information retrieval statistics.For more information, please refer to RPF paper: Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.

Chemical shift Validation

evaluating the accuracy of protein resonance assignments determined by either automated or manual methods,for more information, please refer to AVS paper:
Assignment validation software suite for the evaluation and presentation of protein resonance assignment data