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Testimonials

ACEMD allows to perform state-of-the-art molecular dynamics simulations on your own desktop or server equipped with GPUs. It is user-friendly and through its simplicity for standard simulations, it can be customized through the use of a plugin module to be written in C or in combination with PLUMED.

“ACEMD is without any doubt a versatile program that exploit the full potential of MD simulations, using cost-effective hardware solutions, that can be adapted to every Molecular Modeling laboratory needs.”

“Acellera and ACEMD afforded us a straightforward new tool based on its amazing MD engine performance capable to exploit fully the latest GPU hardwares. It can be easily plugged to extra codes for a maximal versatility and no doubts remains on its usefulness for an atomic scale interpretation of biomolecular NMR data and its specific spectroscopic time-scales.”

“ACEMD is an admirable molecular dynamics tool that clearly holds its promises.”

“ACEMD has provided a significant boost in performance, even a single GPU card out performs several hundred CPU-cores. With 10 cards we can easily generate microsecond level sampling in a few days.”

Scouting

This protocol simulates the target of interest (GPCR, kinase, ion channel, etc.) in a solution of water and a co-solvent, like benzene or any other fragment-like molecule.

During the simulation, the co-solvent molecules interact with the surface of the protein, revealing binding hotspots. These hotspots have been proven to correlate very well with actual pockets.

Furthermore, binding modes for the probes can be extracted, which can prove very valuable, as the binding mode of bigger, drug-like molecules could mirror that of the probe.
We can run multiple different fragments in parallel to conduct a virtual screening campaign.

Steps

  1. Binding site prediction: Identify the most likely binding sites of your target of interest, including orthosteric, allosteric and cryptic sites.
  2. Binding mode prediction: Obtain binding mode predictions and pharmacophoric insights from your co-solvent molecule, which can be used to precisely guide a docking campaign.
  3. Pocket ensemble: For each pocket, we will select the snapshots from the simulation where the pocket is in a “binding-ready” state. This ensemble can be used to model protein flexibility while docking.
  4. Binding pathway: For each pocket, we will provide a trajectory linking the unbound state to the bound state.

    CrypticScout job typically takes only one week to finish (~10 replicas of 80 nanoseconds each).

Use Case

Results of a CrypticScout job for a Ras protein (PDB code:4Q21). At high isovalues, the orange wireframe only highligths the pockets which the probe visited the most (or the longest). One of the identified pockets is the actual binding pocket of the endogenous ligand. The extracted pose for the chosen co-solvent (imidazole) overlaps very well with the actual ligand.

Results

  • A PlayMolecule scene with binding hotspots and binding mode predictions.
  • The full simulations (.xtc and .pdb files).
  • The cloud of hotspots as a .cube file (orange wireframe in the image).
  • An extensive report summarizing the structural insights obtained.
  • For each identified pocket:
    • Binding mode prediction can be used to do pharmacophoric docking or scaffold docking. (.pdb + .sdf)
    • Ensemble of druggable conformations, to model protein flexibility in docking (.pdb files)
    • Binding pathway of the co-solvent molecule from the bulk into the pocket (.xtc file)
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