ROSTLAB - The PROFbval Server

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PROFbval is a method for predicting residue mobility based on amino-acid sequence.

The mobility of a given residue on the protein surface is related to its functional role. Therefore, identification of extremely rigid or flexible residues on the protein surface is helpful for identifying functionally important residues in proteins. A common measure of atom mobility in proteins is B-value data from x-ray crystallography structures. Here we present PROFbval, the first web server to predict normalized backbone B-values from amino-acid sequence. PROFbval can be useful for both protein structure and function predictions. For instance, a biologist can locate potentially antigenic determinants by identifying the most flexible residues on the protein surface. Additionally, a crystallographer can locate residues that potentially have high experimental B-values.

See examples of the input and output of the server.

Developers: Avner Schlessinger & Burkhard Rost, department of Biochemistry and Molecular Biophysics, Columbia University (2005).

Output

Two types of prediction are available:
(i) Two-state prediction result - simply if a residue is predicted to be flexible or not.

Non-strict mode (NS) - most of the residues are flexible; hence, a residue on the surface that is predicted to be rigid is likely to have a functional role.
Strict mode (S) - about a third of the residues are flexible, therefore, a stretch of residues that is predicted to be flexible might be important for the protein function.
Reliability index - the output of the network was converted to reliability index reflecting the strength of the prediction (values 0-9). High value indicates strong prediction. RI_s marks the reliability index of the strict mode and RI_ns marks the reliability index of the non-strict.
Accessibility – solvent accessibility prediction by PROFacc - ‘e’ marks exposed and ‘b’ marks buried. A residue that is predicted to be ≥16% exposed to the surface is defined to be exposed.

(ii) Normalized B-value prediction - the values are normalized so in a given sequence the average value is 0 and the standard deviation is 1. the higher the value the more flexible a residue is predicted to be.

Window size - For smooth output of the predicted value a window size can be given.

In addition to the flexibility predictions the server prints out the 2-state predicted solvent accessibility ('b' marks buried and 'e' marks exposed) as predicted by PROFacc.

Output Format

By default, the results will be in HTML format. However, results in plain text format can also be requested.
The results page will be available to download from our website and only URLs are sent to the users by email unless the user requests the full results being sent directly.

Please Cite:

Method:
Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins. 2005 Oct 1;61(1):115-26.

Server:
Schlessinger A, Yachdav G, & Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 2006 Apr 1;22(7):891-3. Epub 2006 Feb 2.

Contact: Avner Schlessinger