DOI: 10.5061/dryad.z08kprrn0
title: Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold

description: Ion channels play key roles in human physiology and are important targets
 in drug discovery. The atomic-scale structures of ion channels provide
 invaluable insights into a fundamental understanding of the molecular
 mechanisms of channel gating and modulation. Recent breakthroughs in deep
 learning-based computational methods, such as AlphaFold, RoseTTAFold, and
 ESMFold have transformed research in protein structure prediction and
 design. We review the application of AlphaFold, RoseTTAFold, and ESMFold
 to structural modeling of ion channels using representative voltage-gated
 ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8,
 human voltage-gated calcium (CaV) channel – CaV1.1, and human
 voltage-gated potassium (KV) channel – KV1.3. We compared AlphaFold,
 RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3
 with corresponding cryo-EM structures to assess details of their
 similarities and differences. Our findings shed light on the strengths and
 limitations of the current state-of-the-art deep learning-based
 computational methods for modeling ion channel structures, offering
 valuable insights to guide their future applications for ion channel
 research.
description: # Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and
 ESMFold This README file was generated on 2024-03-07 by Vladimir
 Yarov-Yarovoy. ## GENERAL INFORMATION 1\. Title of Dataset: Structural
 modeling of hERG channel: Drug interactions using Rosetta 2\. Author
 Information             A. Principal Investigator Contact Information  
            Name: Vladimir Yarov-Yarovoy                       Institution:
 University of California, Davis              Address: Davis, CA USA  
            Email: [yarovoy@ucdavis.edu](mailto:yarovoy@ucdavis.edu) 3\.
 Date of data collection (single date, range, approximate date): May –
 December, 2023 4\. Geographic location of data collection: Davis, CA USA
 5\. Information about funding sources that supported the collection of the
 data: National Institute of Neurological Disorders and Stroke grant:
 1R61NS127285 National Heart, Lung, and Blood Institute grant: 1R01HL159304
 National Heart, Lung, and Blood Institute grant: R01HL128537  --- 1\.
 Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain 2\. Links to publications that cite or use the data: Phuong
 Tran Nguyen, Brandon John Harris, Diego Lopez Mateos, Adriana Hernández
 González, Adam Michael Murray, and Vladimir Yarov-Yarovoy (2024)
 Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and
 ESMFold. Channels 18(1): 2325032.
 [https://doi.org/10.1080/19336950.2024.2325032](https://doi.org/10.1080/19336950.2024.2325032). 3\. Links to other publicly accessible locations of the data: None 4\. Links/relationships to ancillary data sets: None 5\. Was data derived from another source? No             A. If yes, list source(s): NA 6\. Recommended citation for this dataset: Phuong Tran Nguyen, Brandon John Harris, Diego Lopez Mateos, Adriana Hernández González, Adam Michael Murray, and Vladimir Yarov-Yarovoy (2024) Data from: Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold. Channels 18(1): 2325032. [https://doi.org/10.1080/19336950.2024.2325032](https://doi.org/10.1080/19336950.2024.2325032). Dryad Digital Repository. [https://doi.org/10.5061/dryad.z08kprrn0](https://doi.org/10.5061/dryad.z08kprrn0) ## DATA & FILE OVERVIEW 1\. File List: A)    hNav1.8.zip B)    hCav1.1.zip C)    hKv1.3.zip 2\. Relationship between files, if important: None 3\. Additional related data collected that was not included in the current data package: None 4\. Are there multiple versions of the dataset? No             A. If yes, name of file(s) that was updated: NA                         i. Why was the file updated? NA                         ii. When was the file updated? NA ### DATA-SPECIFIC INFORMATION FOR: hNav1.8.zip 1\. Contains AlphaFold2, RoseTTAFold2, and ESMFold models of human Nav1.8 channel (in Protein Data Bank (PDB) format): * hNav1.8-AF2_rank_1.pdb – top AlphaFold2 model of human Nav1.8 channel.   * hNav1.8-RF2-0.pdb – one of top 5 RoseTTAFold2 models of human Nav1.8 channel.  * hNav1.8-RF2-1.pdb – one of top 5 RoseTTAFold2 models of human Nav1.8 channel.  * hNav1.8-RF2-2.pdb – one of top 5 RoseTTAFold2 models of human Nav1.8 channel.  * hNav1.8-RF2-3.pdb – one of top 5 RoseTTAFold2 models of human Nav1.8 channel.  * hNav1.8-RF2-4.pdb – one of top 5 RoseTTAFold2 models of human Nav1.8 channel.  * hNav1.8-ESMF.pdb – top ESMFold model of human Nav1.8 channel.  2\. Each*.pdb file can be opened using PyMol software ([https://pymol.org/2/](https://pymol.org/2/)) or UCSF Chimera software ([https://www.cgl.ucsf.edu/chimera/](https://www.cgl.ucsf.edu/chimera/)) 3\. Missing data codes: None 4\. Specialized formats or other abbreviations used: None ### DATA-SPECIFIC INFORMATION FOR: hCav1.1.zip 1\. Contains AlphaFold2, RoseTTAFold2, and ESMFold models of human Cav1.1 channel (in Protein Data Bank (PDB) format): * hCav1.1-AF2.pdb – top AlphaFold2 model of human Cav1.1 channel.   * hCav1.1-RF2.pdb – top RoseTTAFold2 model of human Cav1.1 channel.  * hCav1.1-ESMFold.pdb – top ESMFold model of human Cav1.1 channel.  2\. Each*.pdb file can be opened using PyMol software ([https://pymol.org/2/](https://pymol.org/2/)) or UCSF Chimera software ([https://www.cgl.ucsf.edu/chimera/](https://www.cgl.ucsf.edu/chimera/)) 3\. Missing data codes: None 4\. Specialized formats or other abbreviations used: None ### DATA-SPECIFIC INFORMATION FOR: hKv1.3.zip 1\. Contains AlphaFold2, RoseTTAFold2, and ESMFold models of human Kv1.3 channel (in Protein Data Bank (PDB) format): * hKv1.3-AF2_rank_1.pdb – top AlphaFold2 model of human Kv1.3 channel.   * hKv1.3-RF2-m1.pdb – one of top 2 RoseTTAFold2 model of human Kv1.3 channel.  * hKv1.3-RF2-m2.pdb – one of top 2 RoseTTAFold2 model of human Kv1.3 channel.  * hKv1.3-ESMF-m1.pdb – one of top 2 ESMFold model of human Kv1.3 channel.  * hKv1.3-ESMF-m2.pdb – one of top 2 ESMFold model of human Kv1.3 channel.  2\. Each*.pdb file can be opened using PyMol software ([https://pymol.org/2/](https://pymol.org/2/)) or UCSF Chimera software ([https://www.cgl.ucsf.edu/chimera/](https://www.cgl.ucsf.edu/chimera/)) 3\. Missing data codes: None 4\. Specialized formats or other abbreviations used: None