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.
This program can be accessed via the PredictProtein service.
Installation with aptitude (Debian, Ubuntu, etc.)
- If you have not done so until now, add the rostlab repository to the list of your syanptic package manager. This is how it's done: Debian_repository#sources.list.d
- aptitude update
- aptitude (search for rostlab keyring and install by marking the package with a '+' and hit 'g' twice to install)
- aptitude update (to determine all rostlab packages to install)
- aptitude install profBVAL. Here's a step by step guide Debian_repository#Installing_a_package_step_by_step
In order to properly run PROFbval you will need to install the following packages. These will be used to create the required PROFbval input files.
- BLAST - The popular sequence alignment program.
- PROFphd - Secondary structure and solvent accessibility predictor. Package also provides useful conversion utilities see Generating an HSSP Input File .
Generating Input Files for PROFbval
PROFbval takes 3 input files:
- sequence_file - file containing protein amino-acid sequence in fasta format.
- filtered_hssp_file - PSI-BLAST alignment profile file.
- rdbProf_file - Secondary structure and solvent accessibility prediction by PROF in rdb format.
Generating an HSSP Input File
Here is a protocol for converting an alignment to an HSSP profile.
Generating an rdbProf File
Generating an rdbProf file requires generating an HSSP input file. The HSSP input file is used as input to the prof program.
prof <filtered_hssp_file> both numresMin=17 nresPerLineAli=60 riSubSec=4 riSubAcc=3 fileRdb=<rdbProf_file>
Please see the PROFbval man page:
Two types of prediction are available:
- 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.
- Normalized B-value prediction - the values are normalized so in a given sequence the average value is 0 and the standard deviation is 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.
- 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.
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.
Avner Schlessinger & Burkhard Rost, department of Biochemistry and Molecular Biophysics, Columbia University (2005).