Documentation

FORECASTER Suite:

FORECASTER Platform:


Screencasts

FORECASTER Platform:
  • How to run a self docking with FITTED using the Forecaster Platform.

      Video length 2:47

  • How to run a docking with FITTED using the Forecaster Platform from a 2D molecule using CONVERT.

      Video length 2:49

  • How to run a site of metabolism prediction with IMPACTS using the Forecaster Platform

     Video length 1:35

  • How to run a flexible docking with FITTED using the Forecaster Platform from a 2D molecule using CONVERT and from a single pdb file with multiple protein side chain conformations.

      Video length 3:15

  • How to run a flexible docking with FITTED using the Forecaster Platform from a 2D molecule using CONVERT and from multiple pdb files.

      Video length 4:39

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Tutorials

FORECASTER Suite:

FORECASTER Suite 2016 tutorials:

FORECASTER Suite 2014 tutorial:

FORECASTER Web Platform:

FAQs

1. How to define the protein active site How to define the protein active site

The co-crystallized ligand should be used to define the protein active site.

In the case where there is no co-crystallized protein available, it is still possible to predefine an area for the active site. There are two possibilities: the first one is detailed in the user guide and consists to list all the amino acids inside the area; the second is to manually position a probe molecule such as benzene in the center of the area of the active site and to save this molecule as the ligand (mol2 format, to be used in the setup of the protein).

2. Why the layout is wrong? Why the layout is wrong?

Even if we try to have a layout that will display correctly on most internet browers, there are always new versions that we haven't tested or successfully modified our template to support these new versions. Please send us some feedback on your experience with your browser version and OS. You can refer the the user Guide for more details.

3. Reaction Manager doesn't work for my reaction Reaction Manager doesn't work for my reaction

The Reaction Manager can automatically convert a reaction scheme into rules to be used in the combinatorial library action (using the REACT program). However, this tool is still under development and it might be possible that your reaction scheme is not correctly recognized and not converted into proper rules. Contact us with your reaction scheme and we'll provide you the correct rules.

4. Score and energy values in FITTED Score and energy values in FITTED

The score is used to compare different ligands together and the energy is used to identify the best pose for the same ligand. So out of the three runs, one should consider the pose with the best energy and compare this score to other ligands. The mscore is the MatchScore which is a score of the interactions of the ligand and the protein. This matchscore provides information about the complementarity of the ligand and the active site defined as the Interaction Spheres (IS).

5. Java application not loading in browser Java application not loading in browser

When trying to visualize a molecule with either the 2D Sketcher or the 3D OpenAstex viewer, the Java security needs to be set to Medium in order to allow the execution of the application. 1. Go to the Java Control Panel (On Windows Click Start and then Configure Java). 2. Click on the Security tab. 3. Set to Medium. 4. Apply, Close and restart the browser. If using java version 8 or later, add a site exception (example).