profbval - predicts flexibile/rigid residues from sequence
profbval <FASTA_FILE> <RDBPROF_FILE> <HSSP_FILE>
<OUTPUT_FILE[,OUTPUT_FILE,...]> <WINDOW>
<OUTPUT_MODE[,OUTPUT_MODE,...]> <DEBUG>
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.
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>
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.
- 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'
- DEBUG
- Default: 0. Enable with 1.
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
- 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.
- *.profbval
- default output file extension
- /usr/share/doc/profbval/examples
- default precomputed input files directory
- 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