BRAIN Project

The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments).

The BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network.

BRAIN consists of a library or API, and of a Cytoscape plugin.


BRAIN Library

The BRAIN library holds the algorithms and methods for interaction prediction. This library is required to build the BRAIN plugin.

BRAIN Plugin

The BRAIN plugin is a way of running various BRAIN algorithms from the Cytoscape user interface. The plugin runs a prediction analysis and presents the results visually as an interactive Cytoscape network.

Latest Build

Brain Plugin: Version 1.0.5 alpha (2007 May 23) - attachment:brainPlugin.jar

Brain Library: Version 1.0.6 (2007 July 26) - attachment:brainlib-1.1.jar

Brain Dependencies: Additional JARs required by BRAIN - attachment:brainDeps.tar.gz

Release Notes

BRAIN Library 1.1 (2007 July 26)

1.0.6 (2007 June 12)

1.0.5 (2007 May 23)

1.0.4 (2007 May 15)

1.0.3 (2007 April 23)

1.0.2 (2007 April 11)

1.0.1 (2007 February 21)

Running the Plugin


SVN path:

Tagged Releases are available under


Human RefSeq Database (GenPept Format, 2007 Feb 21): attachment:human.protein.gpff.gz

Peptide file (new 1.1 format): attachment:peptide_file_v1.1.txt

A peptide file contains a set of experimentally observed ligands for a given domain-containing query protein. Information in the peptide file includes query protein annotation (database identifiers), domain sequence, ligand sequence, and ligand expression data.

Peptide file conversion script:

Converts peptide files from format version 1.0 to version 1.1. It takes an input file or directory path, and an output directory path.

e.g. ~/data/oldfiles/ ~/data/newfiles/

This will convert all peptide files in ~/data/oldfiles to the new format; converted files are written to the directory ~/data/newfiles/. To convert a single file, provide the path (including filename) to the peptide file in the first argument. If the output directory doesn't exist, it is created. Make sure read permissions are correctly set for the input file/directory, and write permissions are correctly set for the output directory. Paths can be relative or absolute.

For usage, run the script with no arguments.


Java Runtime Environment (JRE) 1.5 or later is required to run LOLA. All other dependencies are included in the download.

Installing and Running

Here's a view of LOLA after opening a PDZ domain project file:


Input Format

LOLA accepts one or more peptide file as shown in the example below. A peptide file describes a protein containing a specific domain, and provides known peptide ligands of this domain obtained by an experimental technique.

The peptide file consists of a Header Section that describes the protein and domain sequence, and a Peptide Section that lists and describes the peptide ligands.


Gene Name       DLG1
Accession       Refseq:NP_004078
Organism        Homo Sapiens (Human)
NCBITaxonomyID  9606
Domain Number   3
Domain Type     PDZ
Interpro ID     IPR001478
Technique       Phage Display High Valency
Domain Range    466-525
PeptideName     Peptide CloneFrequency  QuantData       ExternalIdentifier
1       XLHFWRESSV      66
2       XXRLWKQTSL      3
3       ILKIWRETSL      3
4       KRTIWRETSL      2
A       KNLRSNSMLG      2
6       HLKFWRSTRV      2
7       AHSKWRSTSV      2
8       XXXHRRETTV      1
9       VISRWRQTSL      1
10      TTWLGRQTRV      1
11      SRSSYRETSV      1
12      XXXSRRETSV      1
13      RLFRYRETSL      1
B       PIRKRWTMTL      1
15      XXXNHRETSV      1
16      KIVRWKNTSV      1
17      KHRTWYETSV      1
18      XXXXFKQTSV      1
19      ARPKWRTTRV      1
20      ALPRRRETSV      1

Header Section

Describes the protein, domain, and experiment. Required fields are indicated with a *.

NOTE: This section is in a 2 column format. Field names must be separated from their values with a single TAB character. Multiple TABs or spaces are not accepted.

Peptide Section

Describes the experimentally determined peptide ligands. The peptide sequences must be in multiple alignment format. The sequences should contain no gaps, and should be padded with the X symbol on both sides, where required, such that all sequences have identical length.

NOTE: This section is in a 5-column format. Column headers and values must be separated with a single TAB character. Multiple TABs or spaces are not accepted.

Required fields are indicated with a *.

Using Project Files

To open several peptide files at once, simply link them all in a single project file. A project file is a text file containing the absolute paths of multiple peptide files. Opening the project file in LOLA will open each of the underlying peptide files in a single step, allowing logos to be constructed for multiple profiles.



NOTE: The first line of the project file must contain the text "#ProjectFile".

Future Developments


If you have any questions or feedback, please email Moyez Dharsee at

Software/BRAIN (last edited 2008-01-11 01:48:50 by MoyezDharsee)

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