Department of Computing Science, University of Alberta, Edmonton, AB, Canada.
J Biomol NMR. 2011 May;50(1):43-57. doi: 10.1007/s10858-011-9478-4. Epub 2011 Mar 30.
A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic (1)H, (13)C and (15)N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain chemical shifts (up to 6×) than many other shift predictors. In particular, SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 ((15)N), 0.9959 ((13)Cα), 0.9992 ((13)Cβ), 0.9676 ((13)C'), 0.9714 ((1)HN), 0.9744 ((1)Hα) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. The correlation between SHIFTX2's predicted and observed side chain chemical shifts is 0.9787 ((13)C) and 0.9482 ((1)H) with RMS errors of 0.9754 and 0.1723 ppm, respectively. SHIFTX2 is able to achieve such a high level of accuracy by using a large, high quality database of training proteins (>190), by utilizing advanced machine learning techniques, by incorporating many more features (χ(2) and χ(3) angles, solvent accessibility, H-bond geometry, pH, temperature), and by combining sequence-based with structure-based chemical shift prediction techniques. With this substantial improvement in accuracy we believe that SHIFTX2 will open the door to many long-anticipated applications of chemical shift prediction to protein structure determination, refinement and validation. SHIFTX2 is available both as a standalone program and as a web server ( http://www.shiftx2.ca ).
一种名为 SHIFTX2 的新计算机程序被描述为能够快速准确地从蛋白质坐标数据计算抗磁（1）H、（13）C 和（15）N 化学位移。与它的前身（SHIFTX）和其他现有的蛋白质化学位移预测程序相比，SHIFTX2 的准确性要高得多（相关系数提高了 26%，均方根误差降低了 3.3 倍），比表现最好的程序要好。它还提供了更高的覆盖率（高达 10%），计算速度更快（高达 8.5 倍），并且能够计算比许多其他位移预测器更多种类的骨架和侧链化学位移（高达 6 倍）。特别是，SHIFTX2 能够达到实验观察到的和预测的骨架化学位移之间的相关系数为 0.9800（（15）N）、0.9959（（13）Cα）、0.9992（（13）Cβ）、0.9676（（13）C'）、0.9714（（1）HN）、0.9744（（1）Hα）和均方根误差分别为 1.1169、0.4412、0.5163、0.5330、0.1711 和 0.1231 ppm。SHIFTX2 预测的和观察到的侧链化学位移之间的相关性为 0.9787（（13）C）和 0.9482（（1）H），均方根误差分别为 0.9754 和 0.1723 ppm。SHIFTX2 通过使用大型、高质量的训练蛋白数据库（>190）、利用先进的机器学习技术、结合更多的特征（χ（2）和 χ（3）角、溶剂可及性、氢键几何形状、pH 值、温度）以及结合基于序列和基于结构的化学位移预测技术，实现了如此高的准确性水平。我们相信，随着准确性的显著提高，SHIFTX2 将为化学位移预测在蛋白质结构确定、精修和验证方面的许多预期应用打开大门。SHIFTX2 既可以作为独立程序使用，也可以作为网络服务器（http://www.shiftx2.ca）使用。
