Here are a few links I like to use


The protein data bank (PDB)
The Uniprot database
The IUPHAR database of receptors and ion channels
SRS@EBI, a very convenient tool for database searching

Protein sequence analysis

PredictProtein, a tool for secondary structure prediction
ClustalW2 (EBI server), a multiple sequence alignment tool
Blast (NCBI server), a tool that finds regions of local similarity between sequences


eMolecules, a database of commercially available compounds
SPARC, a tool for pKa prediction


Website of the Institute of Biology, École Normale Supérieure
Website of the Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes
Website of the University of California at Berkeley