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Permeability Workflow

Calculate permeability coefficient and gain valuable kinetic insight into mechanism of passive membrane permeability, in a fraction of time when compared to other simulation techniques. 

The new permeability workflow in the Orion® Small Molecule Discovery Suite helps researchers gain insight into small-molecule drug candidates’ potential chemical absorption and distribution profiles by predicting the speed and manner through which they cross membranes.

The Orion Permeability Floe (guided workflow) can be used early in the drug development process because it leverages a highly parallelizable path-sampling technique to assess permeability at scale. It does not require late-stage molecular synthesis like costly experimental methods, nor does it require prior knowledge of the membrane pathway like thermodynamics-based computational methods.

Orion Permeability Workflows

With the Orion Permeability Floe, researchers get:

Ease of use

Simply input a 2D or 3D structure and be guided through a series of steps that use sophisticated force fields, enhanced sampling methods and MD engines to assess membrane permeability

Valuable mechanistic insight

Predict not only how long it takes for a molecule to cross the membrane, but also what pathways are taken and what happens to a molecule as it traverses the membrane; this may uncover potential structural modifications that could help a drug candidate get across a membrane

Early druggability assessment

Don’t wait until later stages of drug development to assess permeability. Make predictions early on with just 2D structures from a kinetic rate constant. There is no need for a predetermined membrane pathway or lab synthesized molecule, and there’s no need to wait until you have a smaller subset of candidates due to computing constraints

Fast, large-scale calculations

Get results fast by leveraging on-demand AWS compute resources. The Orion Permeability Floe is parallelizable up to thousands of cores and hundreds of GPUs. Current permeability calculations take a few hours and cost a few hundred of dollars per iteration, and the OpenEye team continues to optimize compute times

Reliable science

Trust that the Orion Permeability Floe has been thoroughly tested, showing improved correlation with experimentally predicted permeabilities for a diverse set of molecules, including short-chained alcohols and drug-like molecules, when compared to other computational methods


Have the flexibility to choose different force fields for use with your molecule of interest

Open architecture

Leverage Orion’s Python-based architecture to expand the workflow with third party plug-ins, such as WExplore, Weighted Ensemble (WE)-based string methods, or with a lightweight object-oriented structure analysis library (LOOS).

Permeability Examples

OpenEye's Orion Permeability method can predict how various drugs might cross a membrane. In the examples below, Orion Permeability method predicted various conformational changes for molecules when crossing the membrane. Orion can leverage its cloud-native design to efficiently perform numerous iterations of this calculation to derive a permeability coefficient and identify a dominant pathway, thus providing you with valuable results in a fraction of time when compared to other simulation techniques. 


Orion’s Permeability Floes (guided workflows) using Weighted Ensemble method creates an ensemble of reactive permeation pathways, along with an estimate of the permeability coefficient, to provide a clearer picture of the microscopic underpinnings of small molecule membrane permeation.

Combining Enhanced Sampling with Cloud Computing

With OpenEye's Permeability method, you can gain kinetic insight into mechanism of passive membrane permeability. Giving you a competitive edge in your drug discovery process... faster.

Learn More

To learn more about the Orion Permeability Floe, view the following webinar recordings:

Permeability at Scale: The Weighted Ensemble Method in Orion. (May 2020) Presented by David LeBard, PhD, Senior Scientific Software Developer at OpenEye

How to Exploit Orion as a Scientific Platform? Permeability as a Case Study in Large Scale Floe Development. (Oct 2021) Presented by David LeBard, PhD, Senior Scientific Software Developer at OpenEye


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