OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

OMEGA, Release 2.5.1.4
PSA
Peter Ertl’s, [Ertl-2000], topological polar surface area (phosphorus and sulfur area is optional).
PSA_USE_SandP false "Count S and P as polar atoms"
MIN_2D_PSA 0.0 "Minimum 2-Dimensional (SMILES) Polar Surface Area"
MAX_2D_PSA 205.0 "Maximum 2-Dimensional (SMILES) Polar Surface Area"
See Also:
The PSA theory section in the Molecular Properties and Predictors chapter.
GSK/Veber
Veber’s measure of bioavailability (PSA > 140 or Rotatable bonds >10). [Veber-2002].
GSK_VEBER false "PSA>140 or >10 rot bonds"
Abbott/Martin
Yvonne Martin’s Abbott Bioavailability Score. This is reported as a probability that F>10% in rats. [Martin-2005]
MIN_ABS 0.11 "Minimum probability F>10% in rats"
Pharmacopia/Egan
Egan egg measure of bioavailability (LogP >5.88 or PSA > 131.6). [Egan-2000]
PHARMACOPIA false "LogP > 5.88 or PSA > 131.6"
12.1.5 Aggregators
Aggregators are small molecules that can interfere with assay results by sequestering protein in an aggregation of small
molecules in solution. They appear to have activity in many assays, but in fact are usually not specific inhibitors of
the protein in question. Includes two measures of whether a molecule is one of the aggregators defined by Shoichet et.
al. [McGovern-2003] [Seidler-2003] The first measure, AGGREGATORS, is whether the molecule is an exact match to
one of the approximately 400 published aggregators. The second measure, PRED_AGG, is whether the molecule hits
in Shoichet’s QSAR model for predicting aggregators.
Aggregators
Whether a compound is known or predicted to aggregate in concentrations common in virtual screening.
AGGREGATORS true "Eliminate known aggregators"
PRED_AGG false "Eliminate predicted aggregators"
52 Chapter 12. Filter Files