---
name: "profisis"
section: "1"
platform: "linux"
package: "profisis"
version: "1.0.11-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/profisis"
---

# profisis(1)

protein-protein interaction sites identified from sequence

## 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

## 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*

## AUTHOR

Yanay Ofran and Burkhard Rost

## SEE ALSO

[**prof**(1)](/prof/1.md)