Protein visualization

World index of molecular visualization and modeling software

Visualization on low-end notebooks: Example RasMol

Visualization inside the browser: Example JMol

Visualization using today's graphics cards and OpenGL: Example YASARA
PyMol, Swiss PDB Viewer , VMD

Reading molecules in 100 different file formats: OpenBabel

Protein structure prediction

CASP blind prediction experiments

List of all servers for automated structure prediction

Alignments for building homology models: BLAST/PsiBLAST , GenThreader

Complete homology modeling examples: Phyre, SwissModel

Protein modeling

Similarity search: DALI