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Using the SwissSimilarity Webserver

1. Checking that the server is up and running

If the Web server is up and running, you will receive a "Hello World!" message.

2. Starting a screen

First of all, you need to create a file containing SMILES of your compound of interest. For example, a file called ibuprofen.smi with CC(C)CC1=CC=C(C=C1)C(C)C(=O)O in it. Afterwards, you can launch the screening by using the following command: where:
- ibuprofen.smi is the file containing SMILES of your compound of interest;
- CHEMBL is a library of compounds to screen;
- ECFP is the molecular fingerprinting method used for screening.

Available screening libraries are:
Asinex, AsisChem, CHEBI, CHEMBL, CHEMBL_drug, CHEMBL_clinic, CHEMBL_act, CHEMBL_GPCR, CHEMBL_kinase, CHEMBL_protease, ChemBridge, ChemDiv, DrugBank, Enamine, Enamine_Tang, Glass, HMDB, InnovaPharm, InnovaPharm_Tang, LifeChemicals, LifeChemicals_Tang, LigandExpo, Maybridge, Otava, Otava_Tang, SPECS, TimTec, Vitas, ZINC_drug, ZINC_frag, ZINC_lead.

Available methods for screening:
ECFP, FP2, MHFP6, pharmacophore, ERG, scaffold, GenScaffold, ES5D, E3FP, Combined

If no problem was found and both the method and the library are available, the screening calculation is submitted to the queue of the server. Then, the user is provided with a randomly chosen Session Number. This Session Number will allow the user to check what is the status of the calculation, and later retrieve the results in case of a successful calculation. Here, 403049986 is the Session Number of the submitted screening.

3. Checking the status of a screening

You can check the status of the job using the Session Number that you have received upon submission. If the calculation is pending in the queue waiting for its turn, you will be informed about that, and you will be provided with the number of jobs that are waiting before it in the queue. If the job is currently running, you will be informed about that and the running time will be reported. If the screening is over, you will be also informed that the job is finished.

4. Cancelling a screen

You can cancel the screening that is currently running or pending in the queue. The following command will remove the calculation from the queue of the server:

5. Retrieving the results of a screening

After you have confirmed that your submitted job is finished (see above), you can retrieve the results:

6. Retrieving information regarding the screening

You can get the date, name of the query molecule file, library and method using the following command: