In both predicting protein loop structure and flexible areas in a docking interface, modeling local loop conformation plays a vital role. We address the challenge with a topological manipulation method based on the cyclic coordinate descent (CCD) algorithm. The protein loop conformation sampler (LMbCCD2) presented here allows us to move some key points of the loop toward some specific positions. We test the method's performance on sets of loops, and the results show that LMbCCD2 accurately controls the loop's topology. At last we use LMbCCD2 on flexible protein–peptide docking, and it shows that LMbCCD2 can improve the accuracy of flexible peptide folding and the full docking result.
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