Overview

EON calculates the electrostatic similarity between two small molecules in the form of an Electrostatic Tanimoto (ET) score. EON supports two descriptions of electrostatics: via charge density (by default) and via potential (-potential true) Given a query molecule and a set of interesting molecules, EON will calculate the Electrostatic Tanimoto between each database molecule and the query. Note, that starting from version 3.0, EON does perform an overlay of the input structures using molecular shape and charge density similarity optimization. Since electrostatics calculations require high quality partial charges, EON will calculate new partial charges for the input structures using MMFF94. If the user provides an input file that contains structures with higher-quality partial charges, EON can use them as well (-charges existing).

EON is also dependent on pKa state and formal charges as these have a significant impact on electrostatics. EON now has the ability to adjust both the query and database molecule to a neutral pH model. This feature is on by default, but can be turned off by using appropriate command line flags.

When EON is run in -potential true mode, the best shape and charge density hits are rescored with shape and potential similarity. In doing so the command line flag -num_top_scores (by default equal to 5) controls how many best hits per molecule are being re-scored.

Part of understanding EON results is visualization of the electrostatic grids used in the calculation. Although off by default, when writing EON results to a binary (OEB) file, ET grids can be attached to each molecule and visualized using the EON View mode in VIDA. When running with -writegrid true, for -potential false the charge density grid will be outputted and for -potential true the electrostatic PB potential grid will be added to results.

Since EON calculations can be time-consuming (approximately 1 molecule per second per CPU for the -potential true case), EON can use the same distributed computing technology, Open MPI, that ROCS uses to help distribute the workload across a cluster of machines.