title: A comparison of different functions for predicted protein model quality assessment.
abstract: In protein structure prediction, a considerable number of models are usually produced by either the Template-Based Method (TBM) or the ab initio prediction. The purpose of this study is to find the critical parameter in assessing the quality of the predicted models. A non-redundant template library was developed and 138 target sequences were modeled. The target sequences were all distant from the proteins in the template library and were aligned with template library proteins on the basis of the transformation matrix. The quality of each model was first assessed with QMEAN and its six parameters, which are C_β interaction energy (C_beta), all-atom pairwise energy (PE), solvation energy (SE), torsion angle energy (TAE), secondary structure agreement (SSA), and solvent accessibility agreement (SAE). Finally, the alignment score (score) was also used to assess the quality of model. Hence, a total of eight parameters (i.e., QMEAN, C_beta, PE, SE, TAE, SSA, SAE, score) were independently used to assess the quality of each model. The results indicate that SSA is the best parameter to estimate the quality of the model.
authors.affiliation: Department of Hematology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, 210008, People's Republic of China.
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.affiliation: School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 210009, People's Republic of China. hsfang889@163.com.
authors.forename: Huisheng
authors.initials: H
authors.lastname: Fang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012984:Software; D012997:Solvents / Q000737:chemistry
chemical_list: D011506:Proteins; D012997:Solvents
keywords: Protein structure prediction; QMEAN; Secondary structure agreement