Molecular Dynamics Simulation Services

Acellera’s molecular simulation services provide a fast turnover, low barrier to entry and secure HPC computing infrastructure for obtaining detailed representations of biophysical phenomena occurring on the microsecond to millisecond timescale.

Our molecular simulation service pipeline is highly modular, and can involve as little as a set of production runs or be full studies composed of system preparation, evaluation, MD simulation execution and analysis.

Contact us for more information.

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Molecular Simulation Service

Obtain up to a millisecond of molecular dynamics (MD) data using our patent-pending AceCloud compute infrastructure. Data analysis assistance is optional.

In-Silico Binding Assay

Understand protein-ligand interactions with all atom resolution using our high-throughput molecular dynamics technology. Obtain binding poses, kinetics, binding affinities and binding pathways for your compounds of choice.

Fragment-Based Drug Discovery

Probe the binding properties of your fragment hits. Understand their binding pose, and affinity, as well as the specificity and selectivity of the interactions between the ligands and the target receptor.

Conformer Analysis Assay

Determine the conformer space of small peptides or larger target proteins in terms of their kinetic and thermodynamic fingerprints. Determine structures compatible with NMR data.

Distinctive Features

How does it work?  

What do I need to do?
All we need is a PDB and some information on the conditions. We will then setup everything accordingly, and once approved, we will run the simulations and return the data to you. If you wish, we will also analyze the data and offer an executive report containing important molecular information like clusters, ranking of important states based on thermodynamics and kinetics.
Is this secure?
Our internal cluster is only accessible to Acellera staff. Once acquisition is complete, the data can be accessed electronically or be sent by couriered mail. 
How do I analyze so much data?
Five years ago we began our work in high-throughput molecular dynamics, and over this time period we have worked on a daily basis with simulation data sets several Terabytes in size. The data+analysis service will save you time by putting our expertise at your fingertips. After working up the results, we will issue a customized, in depth report explaining the obtained results.