The US EPA is charged with screening chemicals for their ability to be endocrine disruptors through interaction with the estrogen, androgen and thyroid axes. The agency is exploring the use of high-throughput in vitro assays to use in the Endocrine Disruptor Screening Program (EDSP), potentially as replacements for lower-throughput in vitro and in vivo tests. The first replacement is an integrated computational and experimental model for estrogen receptor (ER) activity, to be used as an alternative to the EDSP Tier 1 in vitro ER binding and transactivation assays and the in vivo uterotrophic bioassay. The ER agonist model uses a set of 16 in vitro assays that incorporate multiple technologies and cell lines and probe multiple points in the ER pathway. Here, we demonstrate that subsets of assays with as few as 4 assays can predict the activity of all 1811 chemicals tested with accuracy equivalent to that of the full 16-assay model. The prediction accuracy against reference chemicals is higher than that of the full chemical set, partly because the larger set contains many chemicals that can cause a variety of types of assay interference There are multiple accurate assay subsets, allowing flexibility in the construction of a multiplexed assay battery. We also discuss the issue of challenging chemicals, i.e. those that can give false positive results in certain assays, and could hence be more problematic when only a few assays are used.