Cn3D allows to view 3D structures in graphyical view
Pymol is a molecule graphyical system with an embedded python interpreter designed for real time visualization
Rasmol is a graphyical interface to view molecules
Spdbv is to view and analyse macromolecules
Biodesigner is to design various molecules
Bodil used to protein structural and functional analysis and to ligand design
MDL Chime show 3D structues and run in browser as a plugin
MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure:
Shadybox, is package with set of library function targeted towards application developers who want a straightforward way to do simple 2D and 3D graph
Raster 3D is ued to generate high quality images of protein
MolMol is a graphyical interface programme
Viewerlite is a software used for view macromolecules in a 3D
WHAT IF is an extensive protein modeling, protein structure analysis, database handler, molecular graphics package
Visual Cloning 2000 is an advanced new vector map drawing and sequence analysis program
SimVector: Automates the production of publication quality graphics of vectors and provides sequence analysis to assist in the design of cloning experiments
Relibase is a web-based tool for searching and analysing protein ligand structures in the PDB