OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

8.1 Introduction
CHAPTER
EIGHT
FILTERING THEORY
Filtering attempts to eliminate inappropriate or undesirable compounds from a large set before beginning to use them
in modelling studies. The goal is to remove all of the compounds that should not be suggested to a medicinal chemist
as a potential hit. This exercise is obviously case dependent, depending on ease of the assay, intended target, personal
bias of the modeller & medicinal chemist, strengths of the company, etc.
To match this need, FILTER’s default filter encapsulates many of the standard filtering principles, such as removal
of unstable, reactive, and toxic moieties. In addition, FILTER allows the customization of the filtering criteria to fit
specific needs.
The criteria for passing or failing a given molecule fall into three categories.
• Physical properties
– Molecular weight
– Topological polar surface area (TPSA)
– logP
– Bioavailability
• Atomic and functional group content
– Absolute and relative content of heteroatoms
– Limits on a very wide variety of functional groups
• Molecular graph topology
– Number and size of ring systems
– Flexibility of the molecule
– Size and shape of non-ring chains
All of the data FILTER generates in filtering molecules can be written to a tab-separated file for easy import into a
spreadsheet. This function allows for combining the values dynamically for a variety of purposes, including, but not
limited to, determining which filter values best fit each project’s needs.
8.1.1 History
When OpenEye’s work on filtering technology began in 2000, it was designed simply to remove compounds with
reactive or otherwise undesirable functional groups. Over the years, the understanding of lead-like and drug-like
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