title: Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology.
abstract: Many template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and for the study of structure-function relationships for proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins under consideration are low-homology. To improve the performance of TBM methods for such targets, a novel model evaluation method was developed here, and named MEFTop. Our novel method focuses on evaluating the topology by using two novel groups of features. These novel features included secondary structure element (SSE) contact information and 3-dimensional topology information. By combining MEFTop algorithm with FR-t5, a threading program developed by our group, we found that this modified TBM program, which was named FR-t5-M, exhibited significant improvements in predictive abilities for low-homology protein targets. We further showed that the MEFTop could be a generalized method to improve threading programs for low-homology protein targets. The softwares (FR-t5-M and MEFTop) are available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html.
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Wentao
authors.initials: W
authors.lastname: Dai
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Tingrui
authors.initials: T
authors.lastname: Song
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Xuan
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Jin
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Lizong
authors.initials: L
authors.lastname: Deng
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Wu
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Taijiao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins