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Molegro Virtual Docker (MVD) - MVD is an integrated platform for predicting protein-ligand interactions.
http://www.molegro.com

MOLMOL - MOLecule analysis and MOLecule display.
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

RasMol & Chime: Molecular Visualization Freeware
http://www.umass.edu/microbio/rasmol/

Swiss-PdbViewer
http://www.expasy.ch/spdbv/mainpage.htm

WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
http://swift.embl-heidelberg.de/whatif/