title: Sorting protein decoys by machine-learning-to-rank.
abstract: Much progress has been made in Protein structure prediction during the last few decades. As the predicted models can span a broad range of accuracy spectrum, the accuracy of quality estimation becomes one of the key elements of successful protein structure prediction. Over the past years, a number of methods have been developed to address this issue, and these methods could be roughly divided into three categories: the single-model methods, clustering-based methods and quasi single-model methods. In this study, we develop a single-model method MQAPRank based on the learning-to-rank algorithm firstly, and then implement a quasi single-model method Quasi-MQAPRank. The proposed methods are benchmarked on the 3DRobot and CASP11 dataset. The five-fold cross-validation on the 3DRobot dataset shows the proposed single model method outperforms other methods whose outputs are taken as features of the proposed method, and the quasi single-model method can further enhance the performance. On the CASP11 dataset, the proposed methods also perform well compared with other leading methods in corresponding categories. In particular, the Quasi-MQAPRank method achieves a considerable performance on the CASP11 Best150 dataset.
authors.affiliation: School of Computer Science, Fudan University, Shanghai 200433, People's Republic of China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Jing
authors.affiliation: College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, People's Republic of China.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: School of Computer Science, Fudan University, Shanghai 200433, People's Republic of China.
authors.forename: Ruqian
authors.initials: R
authors.lastname: Lu
authors.affiliation: Institute for Data Science and Engineering, East China Normal University, Shanghai 200062, People's Republic of China.
authors.forename: Qiwen
authors.initials: Q
authors.lastname: Dong
mesh_terms: D000465:Algorithms; D000069550:Machine Learning; D008958:Models, Molecular; D021381:Protein Transport; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins