The Protein Databank
http://www.rcsb.org/pdb/
The Protein Databank is an excellent source of 3D macromolecular structure data, the database is searchable both by PDB ID number as well as by keywords.
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CASTp
http://cast.engr.uic.edu/cast/
CASTp is an online software program that analyzes a submitted molecule. According to the CASTp website "the emailed results include measured parameters for pockets, cavities and mouth openings, as well as listing of wall atoms and mouth atoms for each pocket. In addition, a RasMol or mage script sent through email will help you to visualize the pocket of your interest. "
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Complete Human MHC Sequence
http://www.sanger.ac.uk/HGP/Chr6/MHC.shtml
This site is an up-to-date source for the complete sequence of the MHC region of the human genome.
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Protein BLAST
http://www.ncbi.nlm.nih.gov/BLAST/
Widely used, this program compares a submitted sequence to a library of known protein sequences and returns a list of the closest matches.
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SignalP
http://www.cbs.dtu.dk/services/SignalP/#submission
SignalP is an online application used to determine the location of peptide cleavage sites in a given, submitted amino acid sequence.
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DAS
http://www.sbc.su.se/~miklos/DAS/
According to the website, DAS is able "to predict transmembrane segments in any integral membrane protein. DAS is based on low-stringency dot-plots of the query sequence against a collection of non-homologous membrane proteins using a previously derived, special scoring matrix."
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SOSUI WWW Server
http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/sosui.cgi?/sosui_submit.html
By submitting a sequence of 20 to 5000 amino acids to this program, membrane and soluble proteins are able to be discriminated.
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