PROFBVAL(1)

NAME
profbval - predicts flexibile/rigid residues from sequence

SYNOPSIS
profbval <FASTA_FILE> <RDBPROF_FILE> <HSSP_FILE> <OUTPUT_FILE[,OUTPUT_FILE,...]> <WINDOW> <OUTPUT_MODE[,OUTPUT_MODE,...]> <DEBUG>

DESCRIPTION
PROFbval is a neural-network based trained on backbone B-value data from X-ray structure. PROFbval was trained on a sequence unique set of high-resolution protein structures from the PDB.

The mobility of a given residue on the protein surface is related to its functional role. A common measure of atom mobility in proteins is B-value data from x-ray crystallography structures. PROFbval is a method predicting 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.

  Conversion of PSI-BLAST alignment to HSSP format
The most up-to-date procedure can be found at <https://www.rostlab.org/owiki/index.php/How_to_generate_an_HSSP_file_from_alignment#Generating_an_HSSP_profile>.

1. Convert BLAST output to a Single Alignment Format (SAF):
     /usr/share/librg-utils-perl/blast2saf.pl fasta=<query_fasta_file> maxAli=3000 eSaf=1 \
      saf=<saf_formatted_file> <blast_output>

2. Convert SAF format to HSSP:
     /usr/share/librg-utils-perl/copf.pl <saf_formatted_file> formatIn=saf formatOut=hssp \
      fileOut=<hssp_formatted_file> exeConvertSeq=convert_seq

3. Filter results to 80% redundancy:
     /usr/share/librg-utils-perl/hssp_filter.pl red=80 <hssp_formatted_file> fileOut=<filtered_hssp_formatted_file>

  Output format
This description applies to the default output format.

number
    residue number

residue
    residue type

raw raw value of the different between the two output nodes

Bnorm
    predicted normalized B-value 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.

Non-strict mode (NS)
    indicates on a flexible residue. According to the NS mode 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)
    indicates on a flexible residue. According to the S mode 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.

REFERENCES

Schlessinger A, Yachdav G, & Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 2006 Apr 1;22(7):891-3.
Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins. 2005 Oct 1;61(1):115-26.

OPTIONS

FASTA_FILE
    File containing protein amino-acid sequence in fasta format.

RDBPROF_FILE
    Secondary structure and solvent accessibility prediction by PROF in rdb format.

HSSP_FILE
    PSI-BLAST alignment profile file converted to HSSP format.

OUTPUT_FILE
    The name of the final PROFbavl output file. You may give multiple output files. You then probably want to give a list of output modes as well, one for each output file. Separate entries with ',' (comma is not allowed in the file name).

WINDOW
    This is the desired smoothing window for the output. The method was trained on window of 9.

OUTPUT_MODE
    PROFbval can create output files in different formats for different purposes. The default output mode for the package is 6. You may give multiple output modes. You then probably want to give a list of output files as well, one for each output mode. Separate entries with ','.

    Modes: '-1', '0', '1', '2', '3', '4', '5', '6', 'snap', 'snapfun'

    5   For metadisorder(1)

    snap
    snapfun
        For snapfun(1)

DEBUG
    Default: 0. Enable with 1.

EXAMPLE
 profbval /usr/share/doc/profbval/examples/cad23.f /usr/share/doc/profbval/examples/cad23-fil.rdbProf /usr/share/doc/profbval/examples/cad23-fil.hssp cad23.profbval 9 6

ENVIRONMENT

PROFBVAL_ROOT
    The directory used to look up ./scr/createDataFile.pl, ./scr/PROFbval.pl and ./nn_files/jct.in. If unset /usr/share/profbval is used.

FILES

*.profbval
    default output file extension

/usr/share/doc/profbval/examples
    default precomputed input files directory

NOTES

1. It is recommended to create the profiles using 3 iteration of PSI-BLAST against big database
2. It is also recommended to filter the hssp files using hssp_filter.pl from the Prof package using the following command: perl hssp_filter.pl hssp_file red=80

AUTHOR

A. Schlessinger <avnersch@gmail.com>

SEE ALSO
Main website
    <http://www.predictprotein.org/>