title: ResQ: An Approach to Unified Estimation of B-Factor and Residue-Specific Error in Protein Structure Prediction.
abstract: Computer-based structure prediction becomes a major tool to provide large-scale structure models for annotating biological function of proteins. Information of residue-level accuracy and thermal mobility (or B-factor), which is critical to decide how biologists utilize the predicted models, is however missed in most structure prediction pipelines. We developed ResQ for unified residue-level model quality and B-factor estimations by combining local structure assembly variations with sequence-based and structure-based profiling. ResQ was tested on 635 non-redundant proteins with structure models generated by I-TASSER, where the average difference between estimated and observed distance errors is 1.4Å for the confidently modeled proteins. ResQ was further tested on structure decoys from CASP9-11 experiments, where the error of local structure quality prediction is consistently lower than or comparable to other state-of-the-art predictors. Finally, ResQ B-factor profile was used to assist molecular replacement, which resulted in successful solutions on several proteins that could not be solved from constant B-factor settings.
authors.affiliation: School of Mathematical Sciences, Nankai University, Tianjin 300071, China; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Jianyi
authors.initials: J
authors.lastname: Yang
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: zhng@umich.edu.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: B-factor profile; local error estimation; model quality evaluation; protein structure prediction