You can run simple experiments on desktops and laptops. There are no CPU requirements, but we do recommend your desktop or laptop have at least 4GB of RAM.

If you are screening many compounds or running multiple virtual experiments simultaneously, we recommend having an appropriate desktop or server solution. If you are unsure, please contact us with your specific questions.

This is likely due to a user not having the necessary permission for running the software. We highly recommend a user had read/write permissions in their account for the software to run properly.

If your permissions are correctly set up and the software still won’t execute, please contact us at info@molecularforecaster.com with the e-mail header “Software won’t execute”, followed by a description of your operating system and your account permissions.

Our Java-based GUI requires Java 1.6, 1.7 or 1.8 (Java Runtime Environment 8). The Windows installer will automatically install the necessary Java requirements, whereas on Linux and MacOS it is the user’s responsibility to ensure they have the necessary Java framework.

If you still have problems running the Java interface even if your prerequisites are installed, you can use the portable Java interface we ship with our software.

The protein active site is automatically determined by ProCESS if a ligand is present in the PDB structure. Alternatively, you can define your own active site using the following keywords:

AutoFind_Site                                                                 N

Binding_Site                        number-of-residues [be as exhaustive as possible]
                                                                             residue-#1_name [this must be the 3 letter amino acid name followed by the number i.e., ASP000]
                                                                             residue-#2-name

Grid_Center            x y z [the centre of the cavity you want to define, Cartesian coordinates]

For more options see “Parameter” below.

Fitted uses several metrics to define the quality of the binding poses it generates.

Energy is a measure of the binding affinity of a ligand to the target. The lower the energy, the better. In Fitted, the lowest energy binding pose is considered the best one.

RankScore is a set of scoring functions which are based on energy terms and other terms which are all scaled to better model the observed binding free energies.

MatchScore is a measure of how well the ligand fits inside the active site, based on the interaction sites generated by ProCESS. The higher the score (i.e., more positive), the better the ligand matches the protein interaction sites.

FITTED_Score is a composite score based on RankScore and MatchScore. It thus provides a measure of how the ligand interacts with the active site from an energetic and geometric point of view. It should be the metric of choice when ranking compounds.

Note: Comparing energies and scores of ligands between different targets has little to no meaning. These metrics should be used to rank ligands within the same target.