Acid-sensing ion channel-1 (ASIC-1) is a proton-gated ion channel implicated in nociception and neuronal death during ischemia. Recently the first crystal structure of a chicken ASIC was obtained. Expanding upon this work, homology models of the human ASICs were constructed and evaluated. Energy-minimized structures were tested for validity by in silico docking of the models to psalmotoxin-1, which potently inhibits ASIC-1 and not other members of the family. The data are consistent with prior radioligand binding and functional assays while also explaining the selectivity of PcTX-1 for homomeric hASIC-1a. Binding energy calculations suggest that the toxin and channel create a complex that is more stable than the channel alone. The binding is dominated by the coulombic contributions, which account for why the toxin-channel interaction is not observed at low pH. The computational data were experimentally verified with single channel and whole-cell electrophysiological studies. These validated models should allow for the rational design of specific and potent peptidomimetic compounds that may be useful for the treatment of pain or ischemic stroke.Acid-sensing ion channels are a subfamily of the epithelial sodium channel/degenerin family of proteins (1). The proteins in this family share a general topology; each member has two transmembrane-spanning domains, relatively short intracellular N and C termini, and a large extracellular loop containing multiple cysteine-rich domains. These proteins interact with themselves and other family members to form ion channels with unique properties (1, 2). The channels formed are all functionally linked by sensitivity to the small molecule inhibitor amiloride and a general selectivity for conducting sodium despite a sequence identity ranging from 15 to 60% across the family. The epithelial sodium channel/degenerin proteins are important for many physiological and pathophysiological processes. For example, ␣␥-epithelial sodium channel channels expressed in the kidney are important in blood pressure homeostasis, whereas homomeric ASIC-1 channels found in neurons are implicated in nociception and neuronal death during ischemia (1, 3).Using fluorescence detection size exclusion chromatography, Jasti et al. (4) found that homomeric chicken acid-sensing ion channel-1 (ASIC-1) 2 could be crystallized and described the structure of a homomeric cASIC-1 channel lacking intracellular domains and in a nonfunctional state. Unfortunately chicken ASICs are very poorly characterized either pharmacologically or functionally. As crystallization of integral membrane proteins is a challenging technique, obtaining crystal structures of the human members of this family may not be feasible. Despite species difference of just a few amino acids, there may be clinically relevant variations between ASIC homologs (5).This work used homology modeling to deduce structures of the human ASICs. These models were evaluated using structural verification suites and validated using in silico inhibitor docking to r...