The present study aimed at determining the functional characteristics of anti-neuroexcitation peptide II (ANEPII). The depressant insect toxin ANEPII from the Chinese scorpion Buthus martensii Karsch had an effect on insect sodium channels. Previous studies showed that scorpion depressant toxins induce insect flaccid paralysis upon binding to receptor site-4, so we tried to predict the functional residues involved using computational techniques. In this study, three-dimensional structure modeling of ANEPII and site-4 of the insect sodium channel were carried out by homology modeling, and these models were used as the starting point for nanosecond-duration molecular dynamics simulations. Docking studies of ANEPII in the sodium channel homology model were conducted, and likely ANEPII binding loci were investigated. Based on these analyses, the residues Tyr34, Trp36, Gly39, Leu40, Trp53, Asn58, Gly61 and Gly62 were predicted to interact with sodium channel receptor and to act as functional residues.