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ResQ: An Approach to Unified Estimation of B-Factor and Residue-Specific Error in Protein Structure Prediction

Yang, Jianyi, Wang, Yan, Zhang, Yang
Journal of Molecular Biology 2016 v.428 pp. 693-701
biologists, models, pipelines, prediction, protein structure, proteins
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.