<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few
protein complexes are deposited in the PDB with respect to the great amount of
interaction data coming from high-throughput experiments (two-hybrid or affinity
purification of protein complexes and mass spectrometry). Nevertheless, we can rely
on computational techniques for the extraction of high-quality and information-rich
data from the known structures and for their spreading in the protein sequence space.
We describe here the ongoing research projects in our group: we analyse the protein
complexes stored in the PDB and, for each complex involving one domain belonging
to a family of interaction domains for which some interaction data are available, we
can calculate its probability of interaction with any protein sequence. We analyse the
structures of proteins encoding a function specified in a PROSITE pattern, which
exhibits relatively low selectivity and specificity, and build <italic>extended</italic> patterns. To
this aim, we consider residues that are well-conserved in the structure, even if their
conservation cannot easily be recognized in the sequence alignment of the proteins
holding the function. We also analyse protein surface regions and, through the
annotation of the solvent-exposed residues, we annotate protein surface patches via a
structural comparison performed with stringent parameters and independently of the
residue order in the sequence. Local surface comparison may also help in identifying
new sequence patterns, which could not be highlighted with other sequence-based
methods.</p>
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Comp Funct Genomics. 2003 Jul; 4(4):416-419