Self Organising Maps for the Analysis of Molecular Dynamics Data

Processes data from Molecular Dynamics simulations using Self Organising Maps. Features include the ability to read different input formats. Trajectories can be analysed to identify groups of important frames. Output visualisation can be generated for maps and pathways. Methodological details can be found in Motta S et al (2022) . I/O functions for xtc format files were implemented using the 'xdrfile' library available under open source license. The relevant information can be found in inst/COPYRIGHT.

SOMMD

Self Organising Map for analysis of Molecular Dynamics data

Features

SOMMD provides functions to processes data from Molecular Dynamics simulations using Self Organising Maps. Features include the ability to read different input formats such as pdb, gro, dcd and xtc files. Trajectory can be analysed to identify groups of important frames.

Installing SOMMD

For the majority of users we recommend the use of the last stable release available from CRAN. To install from within R issue the command:

#!r
install.packages("SOMMD", dependencies=TRUE)

Citation

To cite SOMMD in publications use:

Motta, S., Callea, L., Bonati, L., Pandini, A. (2022). “PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations.” Journal of Chemical Theory and Computation, 18(3), 1957-1968. doi:10.1021/acs.jctc.1c01163 https://doi.org/10.1021/acs.jctc.1c01163.