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Integration with third party tools

Molecular Discovery is committed to providing customers with the greatest value for their licensed products. For this reason, we are collaborating with leading solution providers to integrate our products in existing infrastructures.

Please contact us for any further inquiry about your specific integration needs.

Pipeline Pilot

Thanks to the Accelrys Independent Software Vendors (ISV) Program, we are proud to provide a full set of Pipeline Pilot® components for MoKa, MetaSite, and VolSurf+.

For further information, feel free to have a look at our PP integration white paper


There are four components available for MoKa:

  1. pKa
  2. Ionize Molecule at pH
  3. Enumerate Ionization States
  4. Enumerate Tautomers

The first MoKa component directly replaces the SciTegic "pKa" component and the example below illustrates piping structures from the SD Reader component into the MoKa pKa component before outputting all sites. The Atom Properties component then assigns the pKa values to the atom labels before the results are shown in a table viewer.

The remaining MoKa components also directly replace the SciTegic equivalent "Ionize Molecule at pH", "Enumerate Ionization States", and "Enumerate Tautomers"


There are two components available for MetaSite:

  1. MetaSite SoM Prediction
  2. Enumerate Metabolites

The first component uses the MetaSite method to predict the "site of metabolism" probability for each atom in each structure, according to a range of Cytochrome P450 enzymes. The specific Cytochrome can be changed under the CYP Models property, and options include: CYP1A1, CYP1A2, CYP2B6, CYP2C19, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP3A5, LIVER, SKIN, BRAIN. Other options include changing the protonation policy on the molecule and the conformational sampling that is applied before the method is applied.

The second "Enumerate Metabolites" component uses the MetaSite method to predict the site of metabolism probabilities for each atom, then the most likely sites are subjected to 22 reaction mechanisms to produce the enumerated metabolites. This component contains the additional parameter "Limit" which filters the enumerated metabolites to output the top N most probable metabolites.


There is one component available for VolSurf+:

  1. VolSurf+ Descriptors

The component uses VolSurf+ to calculate 128 descriptors that are designed for modelling ADME phenomena. Six of these descriptors are based on models of Protein Binding, Volume of Distribution, Caco2 cell permeability, Skin permeability, Blood-Brain Barrier permeation, and Metabolic Stability.