NAME
SmotifTF Template-free Modeling Method
SYNOPSIS
SmotifTF carries out template-free structure prediction using a dynamic library of supersecondary structure fragments obtained from a set of remotely related PDB structures.
PRE-REQUISITES
The Smotif-based modeling algorithm requires the query protein sequence as input.
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-version.tar.gz
cd SmotifTF-version/
perl Makefile.PL PREFIX=/home/user/MyPerlLib/
make
make test
make installSETUP 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/MyPerlLib/share/perl5/SmotifTF-version/smotiftf_config.ini
MODELING ALGORITHM STEPS
----------------------------------------------------
|First run the Pre-requisites: |
| Psipred, HHblits+HHsearch, Psiblast, |
| Delta-blast |
| |
| Single-core job |
| Usage: perl smotiftf_prereq.pl --step=all |
| --sequence_file=1zzz.fasta --dir=1zzz |
----------------------------------------------------
----------------------------------------------------
| Step 1: |
| Compare Smotifs |
| |
| Multi-core / cluster job |
| Usage: perl smotiftf.pl --step=1 --pdb=1zzz |
----------------------------------------------------
----------------------------------------------------
| Step 2: |
| Rank Smotifs |
| |
| Multi-core / cluster job |
| Usage: perl smotiftf.pl --step=2 --pdb=1zzz |
----------------------------------------------------
----------------------------------------------------
| Step 3: |
| Enumerate all possible combinations of |
| Smotifs (about a million models) |
| |
| Multi-core / cluster job |
| Usage: perl smotiftf.pl --step=3 --pdb=1zzz |
----------------------------------------------------
----------------------------------------------------
| Step 4: |
| Rank enumerated structures using a |
| composite energy function |
| |
| Single-core job |
| Usage: perl smotiftf.pl --step=4 --pdb=1zzz |
----------------------------------------------------
----------------------------------------------------
| Step 5: |
| Run Modeller to generate top 5 complete |
| models |
| |
| Single-core job |
| Usage: perl smotiftf.pl --step=5 --pdb=1zzz |
----------------------------------------------------HOW TO RUN THE MODELING ALGORITHM
1. If installed locally, provide the correct path name to the SmotifTF perl library in this perl script (line 14).
2. Create a subdirectory with a dummy pdb file name (eg: 1abc or 1zzz).
3. Put the query fasta file (1zzz.fasta) in this directory.
4. Run the pre-requisites first. This runs Psipred, HHblits+HHsearch, Psiblast and Delta-blast. Input is the query sequence in fasta format and the outputs are (a) dynamic database of Smotifs and (b) the putative Smotifs in the query protein. These are used in the subsequent modeling steps. Follow the instructions given in smotiftf_prereq.pl. For more information about the pre-requisites use: perl smotiftf_prereq.pl -help
Usage: perl smotiftf_prereq.pl --step=all --sequence_file=1zzz.fasta --dir=1zzz5. After the pre-requisites are completed, run steps 1 to 5 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. For more information use: perl smotiftf.pl -help
Usage: perl smotiftf.pl --step=[1-5] --pdb=1zzz6. To run steps 1-5 together use: perl smotiftf.pl --step=all --pdb=1zzz
7. Use multiple-cores or clusters as available, for steps 1 & 3 above. These are slow and require a lot of computational resources.
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 or all (to run all steps consecutively)
- --pdb
-
Give 4-letter dummy pdb_code directory, where all input/output are stored.
DESCRIPTION
SmotifTF will carry out template-free structure prediction of a protein from its sequence to model its complete structure using the Smotif library.