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MutInf is an analysis package written in Python. inline C, and R that analyses data from Molecular Dynamics Simulations to identify statistically significant correlated motions and calculate residue-by-residue conformational entropies. Our work has shown that the pattern of mutual information between residues can be used to predict potential allosteric sites, identify couplings between allosteric sites, and identify residues that might be important in mediating these couplings. Recently, we've also included a module to compare conformational ensembles from MD sims or sets of MD sims using the Kullback-Leibler Divergence / Jensen-Shannon Divergence expansion. This is useful for comparing simulations of wildtype/mutant proteins, apo/holo, simulations started from different conformations, etc. Please see McClendon et. al., JCTC, 2012. for more information.
Keywords: allosteric communication, allosteric communication paths, allostery, correlated motions, entropy, Jensen-Shannon Divergence, Kullback-Leibler Divergence, mutual information
This project is an open source release of tools for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. Commercial components have been used in the model construction, mesh generation and flow solver components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC. Discussion forums for the project can be accessed at https://simtk.org/forum/?group_id=188 (or click Advanced -> Public Forums from the links on the left).
Keywords: 1D boundary conditions, blood flow, cardiovascular, finite element, fluid dynamics, image-based geometric modeling, Image segmentation, Mesh generation, vascular