Interactive viewers

SPDBV, Rasmol, VMD, MageView, BallView

Visualisation

Molscript, Raster3D

Automated Modeling

SwissModel, MODELLER

Electron Micrograph Analysis

[EMAN]
[Situs]

MolecularDynamics

TINKER
Gromacs
Amber

ProteinProteinDocking

Structure comparison (servers)

[VAST]
[CE]
[DALI]