Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold
Cite this dataset
Yarov-Yarovoy, Vladimir et al. (2024). Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold [Dataset]. Dryad. https://doi.org/10.5061/dryad.z08kprrn0
Abstract
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.
README: 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
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
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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.
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. Dryad Digital Repository. 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/) or UCSF Chimera software (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/) or UCSF Chimera software (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/) or UCSF Chimera software (https://www.cgl.ucsf.edu/chimera/)
3. Missing data codes: None
4. Specialized formats or other abbreviations used: None
Funding
National Institute of Neurological Disorders and Stroke, Award: 1R61NS127285-01
National Heart, Lung, and Blood Institute, Award: 1R01HL159304-01
National Heart, Lung, and Blood Institute Division of Intramural Research, Award: R01HL128537, Dr. Rose Dixon (V.Y-Y., Co-I) and to Dr. Colleen Clancy