Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold

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 lim..., , , # 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: [[e-mail]](mailto:[e-mail])

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: R01HL12...