Although now days it is easy to find almost anything one would need to find on the Internet, students often want to have a separate list of the sites, used during the course. I always thought that I hardly needed to make such a list, there were only a few sites used during the course. However, when I started to compile the following link list, I understood how wrong I was.
Protein structure tools, databases and other resources
The Protein Databank (PDB) - a depository of protein 3D structures, also cotains information on the entries, like publication, type of experiment (NMR, X-ray crystallography), and much, much more.
PDBe - the European site of the protein data bank. A different type of organization of information, much more exact hits when searching the site for entries.
PDBsum - one of my favorites. A lot of visual information (figures), links to other databases, like the those mentioned here and many more.
CATH - protein domain classification database. Very useful when trying to find evoilutionary relatives, in protein homology modeling of multidomain proteins, etc.
SCOP - Another protein classification database. A slightly different way of calssification, when compared to CATH, and sometimes it may be easier to follow.
SwissPDB viewer - for some reason changed name to Deep View, but I think most people still call it SwissPDB viewer. An excelent graphics visualization program for protein, DNA and RNA structures. Many useful features, the ost important probably being the tools for homology modeling: superposition of structures, snalysis of structure-based sequence alignment, hydrogen bonds, etc. It is also possible to use for preparing graphics representation for talks, reports, etc.
Tutorial on SwissPDB Viewer by Gale Rhodes - Although you may find tutorial material on SwissPDB Viewer on their site, it is often outdated and sometimes not so well written. Gale has also written an excellent introduction to protein crystallography, called Crystallography made crystal clear. You may also try Gale other page, The molecular level, with some additional tutorials.
Swiss-Model Server- Protein homology modeling server used in the tutorials on this site. There are other servers, but I like the connection between this server and SwissPDB Viewer and the fact that there are different modes of modeling and that I easily can influence the process through the SwissPDB Viewer software (sequence alignment correction, energy estimation, etc). Examples of modeling with this server you can find in the homology modeling part.
Sequences and sequence alignment and analysis tools
The Expasy server - General proteomics server for protein analysis. The strongest side in my opinion is the SwissProt database, which has changed name to UniProt, Prosite and all the resources related to sequence and function analysis. Very good annotation with a lot of links, etc. The use of these databases is decribed in the sequence alignment chapter.
InterPro protein sequence analysis and classification - According to their website, "InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites". This site is extremely useful, e.g., in homology modeling, as described in the tutorial on homology modeling. But it is also useful for finding general functional information on a certain protein.
CLUSTALW2 is used for sequence alignment. Although there are many sites, which use this software, my preference is the EBI server (European Bioinformatics Institute). It provides a lot of options for running the alignment, which I find very useful for teaching purposes.
Jalview - the best multiple sequence alignment editor I know. To get all the features, it is best to download the program and install it on your own computer. You can always start Jalview when you use the sequence alignment server at EBI.
Crystallography related links