Where can I free download on the web a Sequence of Amino Acid
(=protein) database aimed for machine learning ?  This base should
associate a sequence of amino acids with chemical property of the
corresponding protein. The idea is to use cutting edge data mining
technology to infer chemical properties from sequences.

Swiss-Prot ( http://au.expasy.org/sprot/ ) is probably the best
protein database.  You can first search by sequence (you can do this
with the full-text search at
http://au.expasy.org/cgi-bin/sprot-search-ful ) to find the name of
the protein, and then the entry for each protein contains all that is
known about its structure and function, including references.  This
information focuses more on biological relevance than raw chemical
properties, but it is full of useful information that connects a given
protein sequence to function.


If you're interested in structure, the Protein DataBank is the proper
tool.  http://www.rcsb.org/pdb/