NIH MBI Laboratory for Structural Genomics and Proteomics

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Structural Analysis and Verification Server

How Long does it take ?

Depending on how many programs you select to use, this server can take several minutes to run. It also depends on how many residues there are in the protein you submit. SFCheck, in particular, takes a couple of minutes to run itself, even with a medium sized structure.

The following table is provided to indicate typical lengths of time to run the 5 programs which require only the PDB: PROCHECK,WHAT_CHECK,ERRAT,VERIFY_3D,PROVE
Time required (updated July 12, 2006)
# of residues ERRAT aloneERRAT + PROVE + Verify_3DPROCHECK + WHATCHECKALL 5
1GCN
29
1.4 s
3 s
19 s
21 s
1SDF
75
1.8 s
4 s
22 s
27 s
3LZM
164
1.8 s
5 s
51 s
57 s
3SEB
238
1.8 s
6 s
60 s
66 s
1EZM
301
1.7 s
5 s
67 s
71 s
1CEM
363
2.3 s
6 s
83 s
90 s
3TMK
534 (2 chains of 217)
4 s
14 s
342
356 s

How SAVES works

SAVES is a server for analyzing protein structures for validity and assessing how correct they are. It utilizes 6 programs for doing this:

Structure Factor data is also analyzed using the program:

Each of these programs produces large amounts of data that may or may not be useful in determining if any problems exist with a protein model. However, one must look at all of the output information in order to find where any problems are being reported. A useful application would be to have all of the output from all of the programs displayed on a single page. In this way a user could quickly exam all of the information produced from these programs and easily see where problems may exist.

This server is designed to run all of the programs and present the user with all of the data on a single page. Users do not have to run all validation programs, however. Users are presented with a page where they can select which programs to run. Or, a user can push the button on the front corresponding to the validation program that they want to run and run that one alone.

The evaluations the server makes of the outputs of each program are labeled by a simple 3 color scheme:

GOOD: SATISFACTORY
WARNING: INSPECTION SUGGESTED
ERROR: INSPECTION RECOMMENDED

If the output or a section of the output satisfies the conditions the server has for that validation program, then the resulting page will show green boxes. If the validation program returns an error state, then the box will be red. Otherwise, the box will be orange indicating a warning.

Input Files

Any <HTML> tags within the input pdb file are removed along with the content between the tags. This allows people to use .ent files obtained from the PDB as input to SAVES. Furthermore, the input pdb file can have any extension.

The Structure Factor file should be in the .mtz (CCP4) format only. In the future we hope to allow users to submit CNS formatted files.

The Conditions

SAVES responds to the following conditions for each validation program and returns the corresponding color to the output page.
SFCHECK
Amino acid poisitions in the structure get a red flag if
1) shift of backbone is greater than 1.5
2) density correlation of backbone is less than 0.90
3) density index of backbone is less than 0.5
4) B-factor of backbone is greater than 60 Angstroms squared
5) connectivity is less than 65%

For each test, a green rating is given if > 95% of the positions pass the test.

GOOD: SATISFACTORY
yellow rating if 90 - 95% of the positions pass the test.
WARNING: INSPECTION SUGGESTED
Red rating if fewer than 90% of the positions pass the test.
ERROR: INSPECTION RECOMMENDED
PROCHECK
One of the many files produced from running PROCHECK is the summary file: file.sum. The first column in this file for each line indicates 1 of 3 things (as described in the file itself): Nothing or Blank
GOOD: SATISFACTORY
+
WARNING: INSPECTION SUGGESTED
*
ERROR: INSPECTION RECOMMENDED
WHAT_CHECK
The output file produced from running WHAT_CHECK is divided up into sections. Each section is identified by 1 of 3 words: NOTE
GOOD: SATISFACTORY
WARNING
WARNING: INSPECTION SUGGESTED
ERROR
ERROR: INSPECTION RECOMMENDED
ERRAT
The data plot produced from running ERRAT contains a percentage of the sequence that is below the 95% limit for each chain in the input structure. This percentage is reported and no color evaluation is made by SAVES.
VERIFY_3D
Using the averaged data points produced for each amino acid in the sequence, the number of times the value is greater than 0.2 is converted into the percentage of the sequence that has positions with values > 0.2. If this percentage is < 20%
GOOD: SATISFACTORY
20 - 45%
WARNING: INSPECTION SUGGESTED
>= 45%
ERROR: INSPECTION RECOMMENDED
PROVE
In the section delimiter identified with "**OUTLIERS", the percent of the number of buried outliers is given. If this number is < 1.0%
GOOD: SATISFACTORY
1-5%
WARNING: INSPECTION SUGGESTED
> 5%
ERROR: INSPECTION RECOMMENDED

About SFCHECK

In order to run SFCHECK properly, the columns of data need to be indicated from the input file as to which ones contain data for F, SIGF, and FREE. The column types are identified by SAVES, however, a user's input file can have more than one column of the same type, thus requiring the user to indicate which ones are to be used by SFCHECK. SAVES will color code the columns that it thinks are the correct ones, but the user will still have to select the columns to be used. This is the only program that requires user input to run properly. Only files in the CCP4 mtz format are accepted.

Run SAVES now



References