From 1e04d5868f177eb639f03889b59d2cba00206578 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sat, 18 Nov 2017 21:01:49 +0000 Subject: Second try to clean spaces in metadata.xml Signed-off-by: Justin Lecher --- sci-chemistry/shiftx2/metadata.xml | 58 +++++++++++++++++++------------------- 1 file changed, 29 insertions(+), 29 deletions(-) (limited to 'sci-chemistry/shiftx2') diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml index 6fee17f87..e35d2bc02 100644 --- a/sci-chemistry/shiftx2/metadata.xml +++ b/sci-chemistry/shiftx2/metadata.xml @@ -6,36 +6,36 @@ Gentoo Chemistry Project - SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical - shifts for proteins using their structural (PDB) coordinates as input. - SHIFTX2 combines ensemble machine learning methods with sequence - alignment-based methods to calculate protein chemical shifts for - backbone - and side chain atoms. SHIFTX2 has been trained on a carefully selected - set of - 197 proteins and tested on a separate set of 61 proteins. Both the - training - and testing sets consisted of high resolution X-ray structures (less - 2.1A) - with carefully verified chemical shifts assignments. SHIFTX2 is able to - attain - correlation coefficients between experimentally observed and predicted - backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), - 0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, - 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to - other - chemical shift predictors using the same testing data set indicates that - SHIFTX2 is substantially more accurate (up to 26% better by - correlation - coefficient with an RMS error that is up to 3.3X smaller) than any other - program. +SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical +shifts for proteins using their structural (PDB) coordinates as input. +SHIFTX2 combines ensemble machine learning methods with sequence +alignment-based methods to calculate protein chemical shifts for +backbone +and side chain atoms. SHIFTX2 has been trained on a carefully selected +set of +197 proteins and tested on a separate set of 61 proteins. Both the +training +and testing sets consisted of high resolution X-ray structures (less +2.1A) +with carefully verified chemical shifts assignments. SHIFTX2 is able to +attain +correlation coefficients between experimentally observed and predicted +backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), +0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, +0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to +other +chemical shift predictors using the same testing data set indicates that +SHIFTX2 is substantially more accurate (up to 26% better by +correlation +coefficient with an RMS error that is up to 3.3X smaller) than any other +program. - Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and - David Wishart. (2011) SHIFTX2: significantly improved protein chemical - shift - prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. - doi: 10.1007/s10858-011-9478-4. - +Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and +David Wishart. (2011) SHIFTX2: significantly improved protein chemical +shift +prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. +doi: 10.1007/s10858-011-9478-4. + Enables debug output in the shiftx2 java part -- cgit v1.2.3-65-gdbad