/ 
SmotifTF-0.01
River stage zero No dependents
/ SmotifTF

NAME

SmotifTF Template-free Modeling Method

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

2. HHSuite

3. psi-blast and delta-blast

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.

SmotifTF Download and Installation:

The following components need to be downloaded and installed to run SmotifTF:

1. The software from CPAN (http://)

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

	Modeling algorithm steps: 

    	 ----------------------------------------------------
	    |Step 0:				                             |
	    |	Run Pre-requisites			                     |
	    |	Psipred, HHblits+HHsearch, Psiblast, Delta-blast |
		|													 |
	    |	Single-core job		     	                     |
	    |	Usage: 
		|   perl smotiftf_prereq.pl --sequence_file=4uzx.fasta --dir=4uzx --step=all
	     ----------------------------------------------------

How to run the 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. perl smotiftf_prereq.pl --step=all --pdb=1zzz --chain=A --dir=1zzz

5. Run smotiftf.pl according to instructions.

Results:

Top 5 models are stored in the subdirectory (1abc or 1zzz) as: Model.1.pdb, Model.2.pdb, Model.3.pdb, Model.4.pdb & Model.5.pdb

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 or all

--pdb

Give 4-letter dummy pdb_code

--chain

Give 1-letter chain_id

--havestructure

0 or 1 depending on whether a structure is known for the protein from alternate sources.

DESCRIPTION

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