Scoria: a Python module for manipulating 3D molecular data
Just catching up on reading the literature and came across this interesting python paper in Journal of Cheminformatics. DOI.
Scoria is useful for both analyzing molecular dynamics (MD) trajectories and molecular modeling. For example, we have used beta-version Scoria functions to create large-scale lipid-bilayer models, to construct small-molecules models with improved predicted binding affinities, to measure MD-sampled binding-pocket shapes and volumes , and to develop neural-network docking scoring functions, among other applications. As an additional example, in this manuscript we describe a trajectory-analysis Scoria script that colors the atoms of one protein chain by the frequency of their contacts with a second chain.