The xgbAnalysis package is a tool to find suitable reaction coordinates of biomolecular systems, e.g. proteins, using the XGBoost algorithm that can be found here. Given a trajectory from a molecular dynamics simulation and suitable corresponding states, it evaluates, which of the input coordinates describe the system best, resulting in a low dimensional reaction coordinate of directly interpretable original coordinates. To obtain states for a given trajectorie the prodyna package can be used. A tutorial can be found in docs or online.
The code is published "AS IS" under the simplified BSD2 license. For details, please see LICENSE.
If you use the code for published works, please cite as
Please cite:
- S.Brandt, F. Sittel, M. Ernst, and G. Stock, Machine Learning of Biomolecular Reaction Coordinates, J. Phys. Chem. Lett. 9, 2144, 2018: DOI: 10.1021/acs.jpclett.8b00759
Install the xgbAnalysis package, using the R-devtools package
if ( ! ("devtools" %in% installed.packages())) {
install.packages("devtools")
}
devtools::install_github("moldyn/xgbAnalysis")
library(xgbAnalysis)