(21) Development of Protein Structure Prediction System: Secondary Structure Prediction of Membrane Proteins

This study aims to establish a method to estimate three-dimensional structure of membrane protein based on physical interaction calculation by computer. In the total system for estimating three dimensional structure of protein from its amino acid sequence, we will develop the software system for its first half called "SOSUI", identifies the protein and determine the secondary structure based on hydrophobic interaction to the highest precision possible. SOSUI will be made available as ICOT free software. Specifically, this study will develop two modules based on hydrophobic interaction considering the fact that the biological membrane provides a very hydrophobic environment: (1) module for identifying whether the amino acid sequence interacts with the biological membrane and (2) module for precisely estimating the regions of the amino acid sequence embedded in the membrane.