scipion-chem / scipion-chem-rosetta Goto Github PK

Documentation under development, sorry for the inconvenience

This is a Scipion plugin that offers different Rosetta molecular docking tools. These tools will make it possible to carry out molecular docking experiments both on the surface of proteins, in order to avoid possible protein-protein interactions, and inside proteins, in protein pockets related to their biological activity.

Therefore, this plugin allows to use programs from the ROSETTA software suite within the Scipion framework. You need to download the Rosetta suite files before installing the plugin, see section "Binary Files" for details.

Rosetta is a software suite includes algorithms for computational modeling and analysis of protein structures. In addition, it has implemented several docking tools, that we used here (see Rosetta home page for details).

Current programs implemented:

• score
• make_ray_files
• DARC

The full documentation to the plugin can be found in the official documentation page.

You will need to use Scipion3 to run these protocols.

1. Binary files

Rosetta binaries will NOT be downloaded automatically with the plugin.

The independent download of Rosetta software suite by the user is required before running the programs. The installation path is automatically found between all paths. In case of error, this path or any other of your preference has to be set in ROSETTA_HOME in scipion.conf file.

We recommend to install the last version of Rosetta, 3.12 .

The steps to download the Rosetta files are the following ones:

• Go to Rosetta software page.
• Rosetta is available to all non-commercial users for free and to commercial users for a fee. To download the software a license of Rosetta Software Suite is needed. You can get it here.
• With the license (an user and a key is sent to the email) you can download the file Rosetta <version> source + binaries for Linux - as one bundle.
• Unzip the package and save it where you prefer.
• Go to Rosetta/main and it contains the Rosetta source code, database, unit tests and integration tests. The source code is located in source/src can be compiled with SCons using the following commands (for more details see getting started with Rosetta), with opencl as extra to allow to use GPU:

cd path/to/Rosetta/main/source
sudo apt install opencl-dev
./scons.py -j<NumOfJobs> mode=[debug/release*] extras=opencl [bin]

2. AutoDock dependency

The plugin scipion-chem-autodock is a requirement to run the DARC and make_ray_files programs. Therefore, even though it is not a compulsory requirement, it is highly recommended: (https://github.com/scipion-chem/scipion-chem-autodock)

3. Install the plugin in Scipion

• Install the stable version (Not available yet)

  Through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

  or

scipion3 installp -p scipion-chem-rosetta

• Developer's version

  1. Download repository:

  git clone https://github.com/scipion-chem/scipion-chem-rosetta.git
  

  2. Switch to the desired branch (master or devel):

  Scipion-chem-rosetta is constantly under development and including new features. If you want a relatively older an more stable version, use master branch (default). If you want the latest changes and developments, user devel branch.

  cd scipion-chem-rosetta
  git checkout devel
  

  3. Install:

  scipion3 installp -p path_to_scipion-chem-rosetta --devel