Comparison of membrane protein modeling tools and case study on potassium ion channel

Abstract

Membrane proteins are found in cellular and intracellular membranes and often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane. Although membrane proteins comprise one third of the human genome and interact with more than 50% of the whole set of proteins, only few hundred membrane protein structures have been resolved to date. Unlike other proteins, membrane structures proteins are stabilized through the interaction with solubilizing environments and membrane lipids.

The intent of this study is to provide a comprehensive survey on the existing protein modeling methods and compare their efficiency, efficacy and accuracy in modeling membrane proteins. All surveyed methods will be considered to model potassium ion channel on I-TASSER, MODELLER, PHYRE and SWISS-MODEL. Upon the completion of the comparative study, a recommendation about the applicability of the different modeling tools will be provided.