/ 
SmotifTF-0.02
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/ SmotifTF

NAME

SmotifTF Template-free Modeling Method - The pre-requisites

SYNOPSIS

Please read this document completely for running the SmotifTF software successfully on any local computer.

Pre-requisites:

The Smotif-based modeling algorithm requires the query protein sequence as input. Additionally, if the structure of the protein is known from any alternate resource, then a PDB-formatted structure file is required. This pdb-file can be present in a centralized local directory or a user-designated separate directory.

Software / data:

1. Psipred (http://bioinf.cs.ucl.ac.uk/psipred/)

2. HHSuite (ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/)

3. Psiblast and Delta-blast (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)

4. Modeller (version 9.14 https://salilab.org/modeller/)

5. Local PDB directory (central or user-designated) - updated (http://www.rcsb.org).

Download and install the above mentioned software / data according to their instructions.

Note: Psipred and Psiblast require legacy blast and Delta-blast is a part of the Blast+ package.

Databases required:

1. PDBAA blast database is required (ftp://ftp.ncbi.nlm.nih.gov/blast/db/). 2. HHsuite databases NR20 and PDB70 are required (ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/databases/hhsuite_dbs/)

SmotifTF Download and Installation:

Download SmotifTF package from CPAN:

http://search.cpan.org/dist/SmotifTF/

Installation of the software (also available in the README file):

tar -zxvf SmotifTF-0.01.tar.gz

cd SmotifTF-0.01/

perl Makefile.PL PREFIX=/home/user/SmotifTF-0.01

make

make test

make install

Set up the configuration file:

The configuration file, smotifab_config.ini has all the information regarding the required library files and other pre-requisite software.

Set all the paths and executables in this file correctly.

Set environment varible in .bashrc file:

export SMOTIFTF_CONFIG_FILE=/home/user/SmotifTF-0.01/smotiftf_config.ini

Pre-requisites steps: 

     -------------------------------------------------------
    | Run Pre-requisites:                                   |
    | Psipred, HHblits+HHsearch, Psiblast, Delta-blast      |
    |                                                       |
    | Single-core job                                       |
    | Usage:                                                |
    |   perl smotiftf_prereq.pl --sequence_file=1zzz.fasta  |
    |         --dir=1zzz --step=all                         |
     -------------------------------------------------------

How to run the pre-requisites program:

1. Create a subdirectory with a dummy pdb file name (eg: 1abc or 1zzz).

2. Put the query fasta file (1zzz.fasta) in this directory.

3. Optional: If structure is known, include a pdb format structure file in the same directory. 1abc/pdb1abc.ent or 1zzz/pdb1zzz.ent

4. Run the pre-requisites step first. This runs Psipred, HHblits+HHsearch, Psiblast and Delta-blast. It will then generate the dynamic database of Smotifs and the list of putative Smotifs in the query protein. Usage: perl smotiftf_prereq.pl --sequence_file=1zzz.fasta --dir=1zzz --step=all

5. Next, run smotiftf.pl according to the instructions given there.

Reference:

Vallat BK, Fiser A. Modularity of protein folds as a tool for template-free modeling of sequences Manuscript under review.

Authors:

Brinda Vallat, Carlos Madrid and Andras Fiser.

OPTIONS

-help

Print a brief help message and exits.

-man

Prints the manual page and exits.

--step

1,2,3,4,5,6,7,8 or all

--sequence_file

Give the name of the fasta file.

--dir

Give 4-letter dummy pdb_code or any other directory where the fasta file is present.

DESCRIPTION

SmotifTF will carry out template-free structure prediction of a protein from its sequence to model its complete structure using the Smotif library.