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Peptidic toxins from animal venoms target ion channels and provide useful scaffolds for the rational design of novel channel modulators with enhanced potency and subtype selectivity. Despite recent progress in obtaining experimental structures of peptide toxin\u2013ion channel complexes, structural determination of peptide toxins bound to ion channels in physiologically important states remains challenging. Here we describe an application of RosettaDock approach to the structural modeling of peptide toxins interactions with ion channels. We tested this approach on 10 structures of peptide toxin\u2013ion channel complexes and demonstrated that it can sample near\u2010native structures in all tested cases. Our approach will be useful for improving the understanding of the molecular mechanism of natural peptide toxin modulation of ion channel gating and for the structural modeling of novel peptide\u2010based ion channel modulators.<\/jats:p>","DOI":"10.1002\/prot.26474","type":"journal-article","created":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:45:18Z","timestamp":1675334718000},"page":"872-889","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Structural modeling of peptide toxin\u2013ion channel interactions using\n                    <scp>RosettaDock<\/scp>"],"prefix":"10.1002","volume":"91","author":[{"given":"Diego Lopez","family":"Mateos","sequence":"first","affiliation":[{"name":"Department of Physiology and Membrane Biology University of California Davis  Davis California USA"},{"name":"Biophysics Graduate Group University of California Davis  Davis California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2325-4834","authenticated-orcid":false,"given":"Vladimir","family":"Yarov\u2010Yarovoy","sequence":"additional","affiliation":[{"name":"Department of Physiology and Membrane Biology University of California Davis  Davis California USA"},{"name":"Biophysics Graduate Group University of California Davis  Davis California USA"},{"name":"Department of Anesthesiology and Pain Medicine University of California Davis  Davis California USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,2,14]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.bi.55.070186.004513"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2010.08.021"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aau2486"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.cellbio.16.1.521"},{"key":"e_1_2_9_6_1","doi-asserted-by":"crossref","unstructured":"Attali B. 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