Flib: A Fragment Library Generation Software

Saulo de Oliveira - February - 2015 Current Version: 1.01

1. INSTALLATION

Change to the directory where you have extracted the contents of Flib.tgz and type:

$> cd src
$> make
$> make install

This will generate the executable bin/Flib.

2. DEPENDENCIES

Flib does not require any additional software to be executed.

However, Flib requires four input files and accepts a fifth optional file:

1. PDB_ID.fasta.txt : The fasta sequence of the target.
2. PDB_ID.fasta.ss : The predicted secondary structure of the target as output by PSIPRED
3. PDB_ID.spXout : The predicted torsion angles of the target as output by SPINE-X.
4. PDB_ID.hhr : Threading hits as generated by HHBlits.
5. PDB_ID.homol : A text file listing all the homologs to the target (one PDB_ID per line).

The script scripts/install_dependencies.py can be used to install some of Flib's dependencies.

An example of each of these files for protein 1AIU can be found in the folder examples.

On top of the required input files, Flib also requires a local version of the Protein Data Bank (PDB). All the ".pdb" files should be grouped under the same folder and their IDs should be in lower case.

Local versions of the following software can be incorporated into Flib's pipeline:

1. PSIPRED
2. HHSearch/HHBlits
3. SPIDER-2
4. BLAST

The script scripts/install_dependencies.py can be used to install some of Flib's dependencies.

To generate a SAINT2-compliant library, the Python script scripts/process_new.py should be executed. This script requires Python 2.6 or higher and the Biopython Module.

3. CONFIGURATION

In order to configure Flib, alter the path names on the file runflibpipeline.

Make sure to provide the correct paths to Flib and to the local version of the PDB.

4. RUNNING FLIB

To generate fragment libraries using Flib, you should use the script runflibpipeline as follows:

$> export FLIB=<PATH TO FLIB>
$> $FLIB/runflibpipeline 1AIU

The following example should generate the fragment library file "1AIU.lib".

5. TROUBLESHOOTING

Contact sauloho@gmail.com for any problems you may experience using Flib.