$pdb_code,         $chain,            $smotiffields[2],
 172                 $smotiffields[3],  $smotiffields[13], $smotiffields[11],
 173                 $smotiffields[12], $smotiffields[7],  $smotiffields[8],
 174                 $smotiffields[9],  $geoms[0],         $geoms[1],
 175                 $geoms[2],         $geoms[3]

ps is an array of lines. Eahc lines conatins the followinf values. 2pmz pdb_code, F chain, HH smotif_type 16 smotif residue start 26 loop length 7 ss1 length 7 ss2 length VAKKLLTDVIRSGGSSNLLQRTYDYLNSVEKCDAESAQKV seq HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH ss aaaaaaaaaaaaexebaaaaaaaaaaaaaxabbaaaaaaa ramachandran 13.507326 145.200039 160.665006 226.951454',

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, smotiftf_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 1:                                             |
        |       Run Talos+                                   |
        |       Get SS, Phi/PSi, Smotif Information          |
        |       Single-core job                              |
        |       Usage: perl smotiftf.pl --step=1 --pdb=1zzz  |
        |              --chain=A --havestructure=0           |
         ----------------------------------------------------

             ----------------------------------------------------
        |Step 2:                                             |
        |       Compare experimental CS of Query SmotifS     |       
        |       to theoretical CS of library Smotifs         |
            |       Multi-core / cluster job                         |
            |       Usage: perl smotiftf.pl --step=2 --pdb=1zzz  |
        |              --chain=A --havestructure=0           |
         ----------------------------------------------------

             ----------------------------------------------------
        |Step 3:                                             |
        |       Cluster and rank chosen SmotifS              |
        |                                                                    |
        |       Multi-core / cluster job                     |  
            |       Usage: perl smotiftf.pl --step=3 --pdb=1zzz  |
        |              --chain=A --havestructure=0           |
         ----------------------------------------------------

         ----------------------------------------------------
        |Step 4:                                             |
        |       Enumerate all possible combinations of       |
        |       Smotifs (about a million models)             |
        |       Multi-core / cluster job                     |  
        |       Usage: perl smotiftf.pl --step=4 --pdb=1zzz  |
        |              --chain=A --havestructure=0           |
         ----------------------------------------------------

         ----------------------------------------------------
        |Step 5:                                             |
        |       Rank enumerated structures using a           |
        |       composite energy function                    |
        |       Single-core job                              |  
        |       Usage: perl smotiftf.pl --step=5 --pdb=1zzz  |
        |              --chain=A --havestructure=0           |
         ----------------------------------------------------

         ----------------------------------------------------
        |Step 6:                                             |
        |       Run Modeller to generate top 5 complete      |
        |       models                                       |
        |       Single-core job                              |  
        |       Usage: perl smotiftf.pl --step=6 --pdb=1zzz  |
        |              --chain=A --havestructure=0           |
         ----------------------------------------------------

How to run the program:

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

2. Put the chemical shift input file (in BMRB format) in this directory. Use the filename 1abc/pdb1abcshifts.dat or 1zzz/pdb1zzzshifts.dat for the BMRB formatted chemical shift input file.

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 steps 1 to 6 as given above sequentially. Output from previous steps are often required in subsequent steps. Wait for each step to be completed without errors before going to the next step.

5. To run all steps together use: perl smotiftf.pl --step=all --pdb=1zzz --chain=A --havestructure=0

6. Use multiple-cores or clusters as available, for steps 2, 3 & 4. These are slow and require a lot of computational resources.

7. If structure is known, use --havestructure=1. Else, use --havestructure=0 in all the steps.

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:

Menon V, Vallat BK, Dybas JM, Fiser A. Modeling proteins using a super-secondary structure library and NMR chemical shift information. Structure, 2013, 21(6):891-9.

Authors:

Vilas Menon, Brinda Vallat, Joe Dybas, 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.

cpanm SmotifTF

perl -MCPAN -e shell
install SmotifTF