Protein Loop Modeling

• Main Authors: Chiuan-Jung Chen, 陳權忠
• Other Authors: Cheng-Yan Kao
• Format: Others
• Language: en_US
• Published: 2004
• Online Access: http://ndltd.ncl.edu.tw/handle/24010841335178549773

碩士 === 國立臺灣大學 === 資訊工程學研究所 === 92 === A major limitation of current comparative modeling method is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled, and we call this kind of problem loop modeling problem. There are two difficulties of loop modeling problem; the first one is how to generate a feasible conformation of loop, and the other is to find the closest conformation to the native one. Here we present a method which combine several algorithm to solve these two difficulties describing above. For the first problem, we adopt an algorithm called CCD (Cyclic Coordinate Descent), which iteratively change the phi and phi angles from the start residue to the end residue to make the conformation close. And the other one, we use a simple energy function to evaluate the stability of a given loop conformation, and the search algorithm FCEA to find the lowest energy conformation from the random building conformations. We evaluate this method by predict a test set of 14 loops, and the final RMSD of them are almost between 0.72Å~2.81 Å.