Protein Structure Databases:
Protein Data Bank (PDB)
Protein Data Bank Europe (PDBe)
A database of the known 3D structures (PDBsum)
Biologically relevant Ligand-Protein Binding (BioLiP)
Structural Classification of Proteins (SCOP)
Structural Classification of Proteins (SCOP from Berkeley)
Hierarchical classification of protein domain structures (CATH)

Protein Structure Comparison Services:
EMBL server for Pairwise alignment of protein structures (DaliLite)
PDBeFold - Structure Similarity Search Server (SSM)
Alignment server and databases for structure comparison (CE/FATCAT)
Protein 3D Structure Comparison (TM-align) from Zhang Lab
Protein 3D Structure Comparison (FATCAT) from Godzik Lab

Protein Structure Prediction and Analysis Services:
PSIPRED - Protein Structure Prediction Server
3D-JIGSAW - Comparative Modeling Protein Structure Prediction Server
Phyre2 - Protein Homology/analogY Recognition Engine V 2.0
MolProbity - protein structure validation
PMP - Protein Model Portal

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
ENA - European Nucleotide Archive
IEDB - Immune Epitope Database
BRENDA - The Comprehensive Enzyme Information System
NCBI PubMed
ExPASy - translation of a nucleotide (DNA/RNA) sequence to a protein sequence
EMBOSS Transeq - translates nucleic acid sequences to the corresponding peptide sequence
Reverse Translate - accepts a protein sequence as input and uses a codon usage table to generate a DNA sequence