Protein

PDB - Protein Data Bank

ExPASy - The Expert Protein Analysis System Proteomics Server

EBI - The Macromolecular Structure Database

CATH - Protein Structure Classification

SCOP - Structural Classification of Proteins

PDBsum - A database of the known 3D structures of proteins and nucleic acids

PDB at a glance - hypertext-based classification

Ligand

Ligand Depot - data warehouse to small molecules bound to macromolecules

PubChem - information on the biological activities of small molecules

ChemIDplus - Database of chemicals, synonyms, structures, regulatory list information, and links to other databases

ChemFinder - free chemical searching

ZINC - free database of commercially-available compounds for virtual screening

Kegg Ligand - knowledge on the universe of chemical substances and reactions that are relevant to life

Pocket

CASTp - computed atlas of surface topography of proteins

PDBbind - a collection of experimentally measured binding affinity data for protein-ligand complexes

CLIBE - computed ligand binding energy

MOAD - a subset of the Protein Data Bank containing every high-quality example of ligand-protein binding

Graphics

Jmol - a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry

PyMOL - the best molecular graphics system known

RasMol - a free program which displays molecular structure