profisis - Online in the Cloud

PROGRAM:

NAME

profisis - protein-protein interaction sites identified from sequence

SYNOPSIS

profisis [OPTION]

DESCRIPTION

profisis (ISIS) is a machine learning-based method that identifies interacting residues
from sequence alone. Although the method is developed using transient protein-protein
interfaces from complexes of experimentally known 3D structures, it never explicitly uses
3D infor- mation. Instead, we combine predicted structural features with evolutionary
information. The strongest predictions of the method reached over 90% accuracy in a cross-
validation experiment. Our results suggest that despite the significant diversity in the
nature of protein-protein interactions, they all share common basic principles and that
these principles are identifiable from sequence alone.

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
See description of --outformat option.

REFERENCES

Ofran, Y. and Rost, B. (2007). ISIS: interaction sites identified from sequence.
Bioinformatics, 23(2), e13-6.

OPTIONS

Required parameters

--fastafile
file that contains your sequence in fasta format

--hsspfile
file with hssp data for sequence in --fastafile

--rdbproffile
file with prof output for sequence in --fastafile

--outfile
output file

Optional parameters

--outformat
output format [pp|prval], default=pp

pp PredictProtein format:

Output ::= Header_Line Binary_Out Raw_Out

Header_Line ::= '>' Header_String '\n'

Binary_Out ::= ( Horiz_Sequence '\n' Bin_Pred '\n\n' )+

Horiz_Sequence ::= Amino_Acid_One_Letter_Code{,40}

Bin_Pred ::= [P-]{,40}

'P' marks binding residue.

Raw_Out ::= ( Amino_Acid_Number ' ' Amino_Acid_One_Letter_Code ' ' Prediction_Score '\n' )+

Prediction_Score ::= Integer_Value

See example outputs in /usr/share/doc/profisis/examples.

prval
( 'resn resi predicted_value' )+, e.g.

'1 M 25'
'2 R 36'
...

--debug
--nodebug
Default: --nodebug

--succinct
Succinct output (print no confidence values).

Parameters controlling post processing - these parameters affect only the top part of the
'pp' output format

--gap=int
default=20

--stretch=int
default=5

--crd=int
default=7

--crd-restriction
--nocrd-restriction
Default: --crd-restriction. Use original ($crd = undef) code (--crd-restriction) or
use new ($cr) code (--nocrd-restriction).

EXAMPLES

profisis --fastafile /usr/share/doc/profisis/examples/3A1P_A.fasta --hsspfile /usr/share/doc/profisis/examples/3A1P_A.hssp --rdbproffile /usr/share/doc/profisis/examples/3A1P_A.rdbProf --outfile /tmp/3A1P_A.profisis

ENVIRONMENT

PROFISISCONF
Location of configuration file to use, overriding other configuration files

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