The GOLD installation in Vuori can be used through the Discovery Studio 3.1 molecular modeling program. Discovery Studio does not include the actual GOLD software, but it contains an interface ( or a so called Pipeline Pilot Protocol) that can submit GOLD docking tasks to GOLD program.

You don't have to run Discovery Studio remotely from Vuori in order to use the Discovery Studio GOLD interface. Instead you can set up your locally installed Disocvery Studio 3.1 client to communicate with a Discovery Studio server running in Vuori. Note however, that in the Discovery Studio server, the maximum execution time for single GOLD job is limited to four hours (4h). Thus larger GOLD jobs should be submitted using the GOLD command line interface in Vuori. Another option is to split the docking experiment into sub-experiments that can be executed in less than four hours.

Below are instructions that explain how you can access the DS server at Vuori and then send GOLD jobs. The instructions assume that you have Discovery Studio client (3.1) already installed in your local computer.

ssh port forwarding

The first thing you need to do, is to make the two ports that the Discovery Studio server uses in vuori.csc.fi visible to your local computer. The port numbers to use depend on the Discovery Studio version you are using.

• For Discovery Studio 3.1 these ports are: 9947 and 9948

Note that these are not the default port numbers the DS server uses. Thus you do not need to shut down the locally installed DS server while you are using Vuori.

In linux you can create the port forwarding connection with command:

ssh -l cscusername -f -L 9947:127.0.0.1:9947 -L 9948:127.0.0.1:9948 vuori.csc.fi sleep 14400

In the command above cscusername is replaced with your CSC user account. The sleep 14400 command will keep the connection open for 14400s = 4h.

In Windows the port forwarding can be done with program plink. Plink is part of the putty package

    http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

Once you have plink-installed open DOS-prompt window and give command:

plink -L 9948:localhost:9948 -L 9947:localhost:9947 cscusername@vuori.csc.fi

If you are not able to use plink, you can do the port forwarding with Scientist's User Interface:

• Instructions to use Scientist's User Interface for port forwarding
  

Changing the server in Discovery Studio client

After this, start Discovery Studio normally and select command:

File | Change server...

And set server name to be
  localhost:9948

After this setup your Discovery Studio should sent the jobs, launched by the protocols, to the DS server running in Vuori.csc.fi. We recommend that you use the DS server in Vurska only for GOLD jobs as the server is set up so that GOLD jobs are executed through the batch job system but other jobs are executed in the front node of Vuori that has very limited capacity.

Running GOLD docking task with Discovery Studio

In order to run small molecule docking task with GOLD you first need to read in your protein and ligand structures to Discovery Studio program. Normally your protein structure is in one molecule window and candidate ligands in another molecule window. Both the protein and ligands should include hydrogen atoms and the bond orders should be correct. However, unlike to CDOCKER tool, defining force field types and partial charges for the atoms is not needed.

In addition to the protein structure, you must also define the binding site into which the ligands are docked. This can be done by selecting atoms or defining a sphere with Discovery Studio tool: Define and Edit Binding Site.

The GOLD  interface is found from the Protocols explorer, from folder: Receptor-Ligand Interactions. The name of the protocol is Dock Ligands (GOLD).

Figure 1. Discovery Studio Protocols Explorer.

After selecting this protocol a GOLD parameter menu will open to the right down corner of Discovery Studio interface. In addition to defining receptor, ligands and docking site you can also tune several other docking parameters. When all the parameters are set up then you can launch your GOLD job by pressing the green arrow in the tool bar in the top of the interface or by right-clicking the GOLD parameter menu.

Figure 2. GOLD parameter menu.

When the job has been launched you can see the status of your job in the Jobs explorer. When the job has completed, you can study the results by double clicking the corresponding row in the Jobs menu.

Figure 3. Discovery studio Jobs Explorer.