title: Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach.
abstract: 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 LMbCCD2accurately controls the loop's topology. At last we use LMbCCD2on flexible protein-peptide docking, and it shows that LMbCCD2can improve the accuracy of flexible peptide folding and the full docking result.
authors.affiliation: 1 School of Computer Science and Technology, Soochow University , Suzhou, Jiangsu, China .
authors.forename: Haiou
authors.initials: H
authors.lastname: Li
authors.affiliation: 2 School of Electronical Engineering and Computer Science, University of Ottawa , Ottawa, Ontario, Canada .
authors.forename: Lu
authors.initials: L
authors.lastname: Sun
authors.affiliation: 1 School of Computer Science and Technology, Soochow University , Suzhou, Jiangsu, China .
authors.forename: Sheng
authors.initials: S
authors.lastname: Luo
authors.affiliation: 1 School of Computer Science and Technology, Soochow University , Suzhou, Jiangsu, China .|3 Jiangsu Provincial Key Lab for Information Processing Technologies , Suzhou, Jiangsu, China .
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Xia
authors.affiliation: 1 School of Computer Science and Technology, Soochow University , Suzhou, Jiangsu, China .|3 Jiangsu Provincial Key Lab for Information Processing Technologies , Suzhou, Jiangsu, China .
authors.forename: Qiang
authors.initials: Q
authors.lastname: Lyu
keywords: cyclic coordinate descent; flexible protein docking; loop closure algorithm; loop modeling