Protein Tools
Protein Databank
PredictProtein Server
Protein Structure Prediction Center
Database of Interacting Proteins
Protein-Protein Interaction Server
Database of Macromolecular Movements

Crystallography Teaching Tools
Crystallography 101
Teaching guide for X-ray and Neutron Diffraction
Kevin Cowtan's Picture Book of Fourier Transforms

Crystallographic Tools

HIC-UP: Hetero-compound Information center -Uppsala
PRODRG:  The Dundee PRODRG2 Server
Crystal Twinning Server  
PARVATI: Protein Anisotropic Refinement Validation and Analysis
X-ray Anomalous Scattering
mmCIF: macromolecular Crystallographic Information File
cctbx - Crystallography Computing Toolbox
Solvent Content Server

Structural Analysis Tools

CATH: Protein Structure Classification
DALI:  Comparison of Protein Structures in 3D
PROCHECK Server
Protein Structure Verification-Biotech Server

Miscellaneous Sites
Webcutter 2.0

For University of Chicago Users
University of Chicago
Molecular Biosciences at the University of Chicago
John Crerar Library