Skip to content

Latest commit

 

History

History
111 lines (66 loc) · 3.97 KB

itasser.rst

File metadata and controls

111 lines (66 loc) · 3.97 KB
Raw

I-TASSER

Homology modeling

Description

I-TASSER (Iterative Threading ASSEmbly Refinement) is a program for protein homology modeling and functional prediction from a protein sequence. The I-TASSER suite provides numerous other tools such as for ligand-binding site predictions, model refinement, secondary structure predictions, B-factor estimations, and more. ssbio mainly provides tools to run and parse I-TASSER homology modeling results, as well as COACH consensus binding site predictions (optionally with EC number and GO term predictions). Also, scripts are provided to automate homology modeling on a large scale using TORQUE or Slurm job schedulers in a cluster computing environment.

Installation instructions

Note

These instructions were created on an Ubuntu 17.04 system.

Note

Read the README on the I-TASSER Suite page for the most up-to-date instructions

  1. Make sure you have Java installed and it can be run from the command line with java

  2. Head to the I-TASSER download page and register for an license (academic only) to get a password emailed to you

  3. Log in to the I-TASSER download page and download the archive

  4. Unpack the software archive into a convenient directory - a library should also be downloaded to this directory

  5. Run download_lib.pl to then download the library files - this will take some time:

    /path/to/<I-TASSER_directory>/download_lib.pl -libdir ITLIB

  6. Now, I-TASSER can be run according to the README under section 4

  7. To enable GO term predictions...

    1. under construction...

  8. Tip: to update template libraries, create a new command in your crontab (first run crontab -e), and make sure to replace <USERNAME> with your username:

    0 4 * * 1,5 <USERNAME> /path/to/I-TASSER4.4/download_lib.pl -libdir /path/to/ITLIB

    That will run the library update at 4 am every Monday and Friday.

Program execution

In the shell

To run the program on its own in the shell...

<code>

With ssbio

To run the program using the ssbio Python wrapper, see: :func:`ssbio.protein.path.to.wrapper`

FAQs

  • What is a homology model?

    • A predicted 3D structure model of a protein sequence. Models can be template-based, when they are based on an existing experimental structure; or ab initio, generated without a template. Generally, ab initio models are much less reliable.

  • Can I just run I-TASSER using their web server and parse those results with ssbio?

    • Not yet, but you can manually input the model1.pdb file as a new structure for now.

  • How do I cite I-TASSER?

    • Roy A, Kucukural A & Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5: 725–738 Available at: http://dx.doi.org/10.1038/nprot.2010.5

  • How do I run I-TASSER with TORQUE or Slurm job schedulers?

    • under construction...

  • I'm having issues running I-TASSER...

    • See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!

API

.. automodule:: ssbio.protein.structure.homology.itasser.itasserprep
    :members:


.. automodule:: ssbio.protein.structure.homology.itasser.itasserprop
    :members: