Prediction of Ion Channel Structures and Functions

Creative Bioarray is committed to developing new machine learning and simulation-based techniques and expanding the application of these methods to the structural and functional prediction of ion channels, as well as mechanistic studies, accelerating the design of drugs targeting specific ion channels.

Introduction

Ion channels are widely expressed in organisms and participate in a variety of important physiological processes. They are ideal drug targets for diseases such as central nervous system diseases. However, the study of ion channels is still challenging due to their complex membrane environment and dynamic properties. In recent years, the development of various techniques such as X-ray crystallography and cryo-electron microscopy has facilitated the understanding of the precise structure of ion channels, providing a theoretical basis for structure-based drug design.

The emergence of important computational technologies such as molecular dynamics (MD) simulation provides a powerful method for understanding the relationship between the structure and function of human ion channels, which has been widely used in the determination of ion channel structure and functional research. Advanced simulation and machine learning technologies are helpful to further study the structures and mechanisms at atomic details, enabling fundamental improvements in ion channel-based drug design by increasing the effectiveness and efficiency of computer-aided drug design.

Fig. 1 Computational methods in the structure modeling, mechanistic study, and drug discovery of ion channels. (Zhu, 2022)

Our Services

We focus on the development of calculation methods for single-particle cryo-electron microscopy (cryo-EM) and ion channel function analysis to help our clients realize the prediction of ion channel structure and function. Our services include but not limited to:

• Development of computational approaches for single-particle cryo-EM.
• Cryo-EM image analysis. We provide clients with cryo-EM image analysis to reconstruct the three-dimensional (3D) structure of target channel proteins, which are represented by statistically estimated density maps.
• Cryo-EM structure model construction. We have developed a variety of protein structure prediction methods such as RoseTTAFold to help clients build 3D atomic structure models. We will continue to develop more accurate and efficient de novo structural modeling methods to meet the scientific research needs of our clients.
• Evaluation of the quality of cryo-EM structural model.

• Development of computational methods for functional analysis of ion channels.
  We have developed a variety of computational methods to help clients predict the dynamic response and microscopic interactions of ion channels of interest.
• Prediction of interactions between channels and their auxiliary proteins.
• Prediction of binding affinity.

Applications

• Study on the dynamic nature of ion channels
• Study on the molecular mechanisms of channel functions
• Drug design and development

After years of efforts, Creative Bioarray has made some progress in MD simulation and other computing technologies. We have the strength to provide clients with ion channel structure and function prediction services. If you are interested in our services, please feel free to contact us for more details.

Reference

1. Zhu, Z.; et al. Simulation and machine learning methods for ion-channel structure determination, mechanistic studies, and drug design. Frontiers in Pharmacology, 2022, 13.