Kinch Lisa N, Li Wenlin, Monastyrskyy Bohdan, Kryshtafovych Andriy, Grishin Nick V
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050.
Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390-9050.
Proteins. 2016 Sep;84 Suppl 1(Suppl 1):164-80. doi: 10.1002/prot.25020. Epub 2016 Mar 9.
We present an overview of contact-assisted predictions in the eleventh round of critical assessment of protein structure prediction (CASP11), which included four categories: predicted contacts (Tp), correct contacts (Tc), simulated sparse NMR contacts (Ts), and cross-linking contacts (Tx). Comparison of assisted to unassisted model quality highlighted a relatively poor overall performance in CASP11 using predicted Tp and crosslinked Tx contact information. However, average model quality significantly improved in the correct Tc and simulated NMR Ts categories for most targets, where maximum improvement of unassisted models reached an impressive 70 GDT_TS. Comparison of the performance in the correct Tc category to CASP10 suggested the improvement in CASP11 model quality originated from an increased number of provided contacts per target. Group rankings based on a combination of scores used in the CASP11 free modeling (FM) assessment for each category highlight four top-performing groups, with three from the Lee lab and one from the Baker lab. We used the overall performance of these groups in each category to develop hypotheses for their relative outperformance in the correct Tc and simulated NMR Ts categories, which stemmed from the fraction of correct contacts provided (correct Tc category) and a reduced fraction of correct contacts offset by an increased coverage of the correct contacts (simulated NMR Ts category). Proteins 2016; 84(Suppl 1):164-180. © 2016 Wiley Periodicals, Inc.
我们概述了蛋白质结构预测关键评估(CASP11)第十一轮中的接触辅助预测,其包括四类:预测接触(Tp)、正确接触(Tc)、模拟稀疏核磁共振接触(Ts)和交联接触(Tx)。辅助模型与非辅助模型质量的比较突出显示,在CASP11中使用预测的Tp和交联的Tx接触信息时,整体性能相对较差。然而,对于大多数目标,在正确的Tc和模拟核磁共振Ts类别中,平均模型质量显著提高,其中非辅助模型的最大改进达到了令人印象深刻的70 GDT_TS。将正确的Tc类别中的性能与CASP10进行比较表明,CASP11模型质量的提高源于每个目标提供的接触数量增加。基于CASP11自由建模(FM)评估中用于每个类别的分数组合的组排名突出显示了四个表现最佳的组,其中三个来自Lee实验室,一个来自Baker实验室。我们利用这些组在每个类别中的整体性能,针对它们在正确的Tc和模拟核磁共振Ts类别中的相对优异表现提出假设,这源于提供的正确接触的比例(正确的Tc类别)以及正确接触覆盖率增加所抵消的正确接触比例的降低(模拟核磁共振Ts类别)。《蛋白质》2016年;84(增刊1):164 - 180。© 2016威利期刊公司。