profisis (1)

profisis [\s-1OPTION\s0]

profisis (\s-1ISIS\s0) 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 \s-1HSSP\s0 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 \s-1BLAST\s0 output to a Single Alignment Format (\s-1SAF\s0):

 /usr/share/librg-utils-perl/blast2saf.pl fasta=<query_fasta_file> maxAli=3000 eSaf=1 \
  saf=<saf_formatted_file> <blast_output>

2. Convert \s-1SAF\s0 format to \s-1HSSP:\s0

/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). \s-1ISIS:\s0 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

\s-1PROFISISCONF\s0

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 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

prof\|(1)