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 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.
 Chapter 1 Introduction 11.1 Motivation 1Ab initio approach： 2Database Approach： 31.2 Overview 4Chapter 2 Cyclic Coordinate Descent 62.1 Introduction 62.2 Overview 72.3 Minimize Squared Distances 92.4 The ability of CCD 11Chapter 3 The Family Competition Evolutionary Approach 133.1 Introduction 133.2 Overview 133.3 Family Competition 153.4 Chromosome Representation 173.5 Recombination Operators 18Modified Discrete Recombination： 18BLX-0.5 and Intermediate Recombination： 183.6 Mutation Operators 19Self-Adaptive Gaussian Mutation： 20Self-Adaptive Cauchy Mutation： 20Decreasing-based Gaussian Mutation： 223.7 Adaptive Rules 23A-decrease-rule： 23D-increase-rule： 23Chapter 4 A New Combinatorial loop modeling algorithm 244.1 Overview 244.2 Construct Backbone Conformation 254.3 FCCD：The combinatorial algorithm of FCEA and CCD 254.3.1 Chromosome Representation： 274.3.2 Offspring： 274.3.3 CCD： 284.4 Side-Chain Prediction with Rotamer Library 284.5 Energy function 30Chapter 5 Conclusions 335.1 Test Set 335.2 Energy Function vs. RMSD 335.3 The Search ability of FCCD 365.4 result 385.5 Discussion and Future works 40reference 42Appendix A 45
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