In Silico Binding Assay: Molecular Dynamics For Binding Mode Prediction

Binding mode determination and more

In-Silico Binding Assay (ISBA)

When virtual screening is not enough, ISBA allows the reconstruction of the entire binding process of a ligand to its target,  capturing the formation of water bridges and networks, induced-fit effects, and the opening of cryptic pockets. In a collaboration with Pfizer, ISBA succeded in resolving the binding process where docking failed to produce a pose that could explain the behavior of some mutants.

With our in silico approach, we can sample the binding mode of a ligand to its target in a reasonable amount of time (days). Useful to obtain:

Binding mode prediction with molecular dynamics (in collaboration with Pfizer)

Use Cases

  • Rational drug design: Knowing the binding mode of your ligand is the first step towards structure-based design and lead-optimization.
  • Patent reverse engineering: Although patents disclose the 2D structure of the compound and the target to which it binds, its binding mode might not necessarily be disclosed. We can help you find it.
  • Estimate binding affinity and kinetics: One of the key properties of a drug is its binding affinity. We can estimate KD, Kon and Koff values with Markov state models.
  • Binding pathway: In addition to the binding mode, you will obtain the pathway that the ligand follows from bulk to bound state.


  • A PlayMolecule scene with binding mode predictions and binding pathway.
  • The full simulations (.xtc and .pdb files).
  • An extensive report summarizing the structural insights obtained.

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