Resources for students

PubMed - Access to biomedical literature
PDB - Protein DataBank containing over 100,000 experimentally determined protein structures
UniProt - Curated database of protein sequences cross referenced to structural and genomic databases
PubChem - Curated database of 63,000,000 biomedically relevant chemicals
DrugBank - Detailed data on 7,700 clinical and research drugs and their targets

Biochemistry analysis servers
BLAST - Search protein or DNA sequences against genomic databases
SwissDock - Automated docking of a ligand into protein structure
ProtParam - Calculate physical parameters for your protein sequence, such as UV extinction coefficients, molecular weight, pKa

Chemistry software servers - Search and draw chemical structures. Calculate physical and med chem properties.

Free downloadable software
PyMol - Software for viewing and editing protein structures. Free educational version available.
Avogadro - Software for viewing and editing small molecules. Includes changing file formats and geometry optimization.
ChemSketch - Substitute for ChemDraw. Draw and manipulate small molecules. Calculates physical and med chem parameters. Free academic license.
Marvin Beans - Another substitute for ChemDraw. Easy to use!
ApE Plasmid Editor - Easy to use program for viewing and analyzing DNA sequences, plasmids, and expression constructs