RedMD (Reduced Molecular Dynamics)

RedMD is an open source package for molecular dynamics simulations and normal mode analysis of coarse-grained models of proteins and nucleic acids. Force fields are based on one-bead elastic network models and their extensions.

Surface Diver

Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.

PDC (Potential Derived Charges)

PDC (Potential Derived Charges) is a package to calculate effective charges for macromolecules so that they reproduce the molecular electrostatic potential calculated from the numerical solution of the Poisson-Boltzmann equation.

ION

The ION software determines the distribution of ions around biomolecules using the Poisson model and Metropolis Monte-Carlo algorithm.

BD_BOX

BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms.

GeoStaS

GeoStaS divides a biomolecule (proteins, nucleic acids and their complexes) into dynamic domains based on its different conformations, obtained from experiments or simulations.