HOLLOW facilitates the production of surface images of proteins. Hollow generates fake atoms that identifies voids, pockets, channels and depressions in a protein structure specified in the PDB format.
CafeMol is a general-purpose coarse-grained(CG) biomolecular modeling and simulation software.It can simulate proteins,nucleic acids,lipids and their mixture with various CG models.
QuickLookPDB is the QuickLook plugin for displaying PDB files and provides two visualisation options. plugin can use pymol to quickly render thumbnail images, while the heart of the plugin lies with the integration of a HTML-5 PDB viewer, Jolecule.
RedMD (Reduced Molecular Dynamics) is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics.
BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds.
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.
Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.
ORTEP-III is Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations.Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.
Ortep-3 for Windows developed by Dr. Louis Farrugia is a MS-Windows version of the current release of ORTEP-III
Michael N. Burnett and Carroll K. Johnson,
ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations,
Oak Ridge National Laboratory Report ORNL-6895, 1996.