Protein Structure Databases:
Protein Data Bank (PDB)
Structural Classification of Proteins (SCOP)
Hierarchical classification of protein domain structures (CATH)
A database of the known 3D structures (PDBsum)

Protein Structure Comparison Services:
EMBL server for 3-D protein structure database searches (DALI)
Alignment server and databases for structure comparison (CE/CL)
Protein 3D Structure Comparison (MATRAS)

Protein Structure Prediction Services:
PSIPRED - Protein Structure Prediction Server
3D-JIGSAW - Comparative Modeling Protein Structure Prediction Server
3D-PSSM - Fold Recognition Protein Structure Prediction Server
BioInfo.PL - Polish Bioinformatics Site, MetaServer and other services

Protein Domains and Families Databases:
Pfam - Protein families and alignments database
InterPro - database of protein families, domains and functional sites
PRISM - protein interactions by structural matching
InterDom - database of putative interacting protein domains

Protein Sequence Related Resources:
National Center for Biotechnology Information (NCBI)
UniProt - Universal Protein Resource
NCBI PubMed
ExPASy - translation of a nucleotide (DNA/RNA) sequence to a protein sequence