profisis − protein−protein interaction sites identified from sequence
profisis [ OPTION ]
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.
Ofran, Y. and Rost, B. (2007). ISIS: interaction sites identified from
sequence. Bioinformatics, 23(2), e13−6.
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).
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
PROFISISCONF
Location of configuration file to use, overriding other configuration files
/usr/share/profisis/profisisrc.default
Default configuration file. See this file for a description of the parameters.
/etc/profisisrc
System configuration file overriding values in /usr/share/profisis/profisisrc.default
~/.profisisrc
User configuration file overriding values in /etc/profisisrc
$PROFISISCONF
If this environment variable is set ~/.profisisrc is disregarded and the value of the variable is read for configuration options overriding /etc/profisisrc
Yanay Ofran and Burkhard Rost