Help for the LigTMap server

Submit prediction

1. Input:

You can input your molecule by one of the following ways:

Input your molecule in the SMILES format

Or draw the chemical structure of the molecule

If you have more molecules to predict, you can also upload them using a file. The file should contain one SMILES string per line; maximum 20 molecules are accepted.

2. Prediction options:

LigTMap supports both all-target prediction and class-specific target prediction. If you have an idea of which target class that your molecule targets (e.g. you are working on HIV inhibitor derivatives, or you are only interested in that class anyway), select that class only. Otherwise, you can select multiple target classes or all target classes.

LigTMap performs two-stage analysis: (1) it identifies putative targets by ligand similarity search, (2) it performs docking and computes binding fingerprint to re-rank results based on a combined ligand and binding similarity score. However, since the second stage is computationally expensive (hours to days), hence we recommend invoke the second stage analysis manually after getting the first-stage result.

Reference Run Time (w/o queuing time)	Stage 1 Ligand similarity search	Stage 2 Binding similarity analysis
One molecule prediction against all target classes	3 minutes	60 minutes

Nevertheless, to automatically perform the second stage, you may select the option “Calculate binding similarity”. By default, this option is unchecked.

3. Description (optional):

Provide some descriptions about this job

4. Account name (optional):

Provide your email ID, this serves as the keyword to retrieve all your run results later.

5. Submit:

Your prediction request will be submitted to the server queuing system and wait for the turn to run. Each job is given a unique job ID. Please do:

Bookmark the page

Or write down the job ID

Or remember the email ID you provided for this submission

You may wait the run to complete or you may close the window and just return to our server page to check for the results later.

Due to the heavy server load, we suggest you download the results as soon as possible when they are ready. Prediction results will be kept in the server for one month and may be removed afterwards.

Happy running!

View Result

1. The job summary page includes links to the prediction result of each input molecule.

2. Each input molecule has a detail report of target prediction, listing first the number of predicted protein targets in each class, followed by the list of protein targets. In the target list, the ranking of targets is based on the LigTMap score (if both Stage 1 & 2 were performed) or the Ligand similarity score (if only Stage 1 was performed). Their values range between 0 and 1. A high score indicates a strong ligand and/or binding similarity to the known ligand of that target.

3. The target list table can be filtered by clicking the first target classes table, and sorted by clicking its column header.

4. If binding similarity analysis was not performed, you can select the interested target(s) to run the Stage 2 (docking and binding similarity analysis) prediction. Upon completion, the LigTMap score column will be updated with the new results.

5. To view the result of protein-ligand docking, click the 3D button to open a new browser tag for the 3D display of the docked complex and analysis result of protein-ligand contacts based on the protein-ligand interaction profile (PLIP). Click the PDB button to download the coordinates of the docked complex.

6. Download the target prediction result as CVS file by clicking the symbol at the top of the Target list table.

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