Ubuntu Manpage: profbval - predicts flexibile/rigid residues from sequence

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>